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This page was generated on 2024-05-31 17:02:51 -0400 (Fri, 31 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 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 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on nebbiolo1


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

raw results

Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-05-31 01:40:43 -0400 (Fri, 31 May 2024)
EndedAt: 2024-05-31 01:45:40 -0400 (Fri, 31 May 2024)
EllapsedTime: 296.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-05-31 01:41:27.474][biodb::testContext]
biodb.INFO [2024-05-31 01:41:27.477][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:41:27.478][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-31 01:41:27.479][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:41:27.480][biodb::testContext]
biodb.INFO [2024-05-31 01:41:27.487][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-31 01:41:27.489][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-31 01:41:27.497][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:41:27.499][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-31 01:41:27.500][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-31 01:41:27.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.504][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-31 01:41:27.524][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-31 01:41:27.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.528][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-31 01:41:27.530][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-31 01:41:27.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.533][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-31 01:41:27.535][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-31 01:41:27.536][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-31 01:41:27.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.539][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-31 01:41:27.541][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-31 01:41:27.542][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-31 01:41:27.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.545][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-31 01:41:27.547][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-31 01:41:27.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.550][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-31 01:41:27.552][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-31 01:41:27.553][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-31 01:41:27.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.557][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-31 01:41:27.558][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-31 01:41:27.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.561][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-31 01:41:27.563][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-31 01:41:27.564][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-31 01:41:27.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.567][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:41:27.569][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-31 01:41:27.570][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-31 01:41:27.571][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-31 01:41:27.572][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-31 01:41:27.573][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-31 01:41:27.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.577][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-31 01:41:27.578][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-31 01:41:27.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.582][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-31 01:41:27.583][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-31 01:41:27.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.587][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-31 01:41:27.588][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-31 01:41:27.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.592][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-31 01:41:27.593][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-31 01:41:27.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.596][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-31 01:41:27.598][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-31 01:41:27.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.601][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:41:27.602][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-31 01:41:27.606][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-31 01:41:27.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.610][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-31 01:41:27.611][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-31 01:41:27.612][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-31 01:41:27.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.619][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-31 01:41:27.661][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.698][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-31 01:41:27.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:41:27.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.703][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.704][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.705][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:41:27.706][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:41:27.707][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.708][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-31 01:41:27.709][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:41:27.710][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.711][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.712][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:41:27.712][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:41:27.712][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:41:27.712][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:41:27.712][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:41:27.713][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:41:27.714][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:27.715][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:27.716][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:41:27.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:27.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:27.719][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.720][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.721][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:41:27.722][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:41:27.723][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.724][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.726][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-31 01:41:27.728][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.729][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:41:27.730][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.731][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:41:27.732][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.733][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.734][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.735][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.736][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:41:27.737][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:41:27.738][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.739][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-31 01:41:27.740][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:41:27.741][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.742][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.743][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:41:27.743][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:41:27.743][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:41:27.743][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:41:27.743][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:41:27.744][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:41:27.745][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:27.746][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:27.747][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:41:27.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:27.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:27.750][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.751][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:41:27.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:41:27.753][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.754][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.756][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-31 01:41:27.757][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.758][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-31 01:41:27.759][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.760][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:41:27.761][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.762][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.763][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.764][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.765][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:41:27.766][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:41:27.767][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.769][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-31 01:41:27.769][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:41:27.771][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.771][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.773][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.774][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:41:27.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:27.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:27.776][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:41:27.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:27.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:27.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.780][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:41:27.782][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:41:27.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.784][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.785][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-31 01:41:27.787][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.788][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:41:27.789][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.790][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:41:27.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.792][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.793][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.795][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:41:27.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:41:27.797][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.798][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-31 01:41:27.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:41:27.800][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.801][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:27.802][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.803][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:41:27.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:27.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:27.806][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:41:27.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:27.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:27.809][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:41:27.810][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.811][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:41:27.812][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:41:27.813][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:27.814][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:27.818][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:41:27.819][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.819][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[2024-05-31 01:41:27.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.860][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[2024-05-31 01:41:27.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.879][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[2024-05-31 01:41:27.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:27.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:27.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:27.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:27.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:27.898][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-31 01:41:27.903][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-31 01:41:27.904][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-31 01:41:27.906][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-31 01:41:27.907][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:41:27.908][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-31 01:41:27.910][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-31 01:41:27.911][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-31 01:41:27.912][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-31 01:41:27.914][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-31 01:41:27.915][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:41:27.916][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-31 01:41:27.918][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-31 01:41:27.919][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-31 01:41:27.920][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-31 01:41:27.921][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:41:27.923][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-31 01:41:27.924][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-31 01:41:27.925][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:41:27.927][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-31 01:41:27.928][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-31 01:41:27.929][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-31 01:41:27.931][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-31 01:41:27.932][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-31 01:41:27.933][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-31 01:41:27.935][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-31 01:41:27.936][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-31 01:41:27.937][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-31 01:41:27.939][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-31 01:41:27.940][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-31 01:41:27.941][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-31 01:41:27.943][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-31 01:41:27.944][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-31 01:41:27.946][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-31 01:41:27.947][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-31 01:41:27.948][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-31 01:41:27.950][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-31 01:41:27.956][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-31 01:41:27.957][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-31 01:41:27.959][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-31 01:41:27.960][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-31 01:41:27.961][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-31 01:41:27.962][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-31 01:41:27.964][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-31 01:41:27.965][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-31 01:41:27.966][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-31 01:41:27.968][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-31 01:41:27.969][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-31 01:41:27.970][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-31 01:41:27.972][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-31 01:41:27.973][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-31 01:41:27.974][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-31 01:41:27.975][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-31 01:41:27.977][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-31 01:41:27.978][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-31 01:41:27.979][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-31 01:41:27.981][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-31 01:41:27.982][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-31 01:41:27.983][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-31 01:41:27.985][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-31 01:41:27.986][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-31 01:41:27.987][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-31 01:41:27.989][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-31 01:41:27.990][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-31 01:41:27.991][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-31 01:41:27.992][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-31 01:41:27.994][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:41:27.995][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:41:27.996][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-31 01:41:27.998][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-31 01:41:27.999][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-31 01:41:28.000][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-31 01:41:28.002][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-31 01:41:28.003][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-31 01:41:28.004][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-31 01:41:28.005][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-31 01:41:28.007][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-31 01:41:28.008][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-31 01:41:28.009][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-31 01:41:28.011][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-31 01:41:28.012][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-31 01:41:28.013][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-31 01:41:28.015][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-31 01:41:28.020][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-31 01:41:28.022][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-31 01:41:28.025][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:41:28.026][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.028][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.074][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[2024-05-31 01:41:28.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.097][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[2024-05-31 01:41:28.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.103][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[2024-05-31 01:41:28.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.109][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[2024-05-31 01:41:28.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:41:28.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.135][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-31 01:41:28.144][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:41:28.146][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:28.147][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-31 01:41:28.148][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:28.149][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:41:28.150][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:28.150][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:41:28.151][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:28.152][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:41:28.153][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:41:28.154][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:41:28.155][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:28.156][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-31 01:41:28.157][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-31 01:41:28.158][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-31 01:41:28.159][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-31 01:41:28.160][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:41:28.160][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:41:28.161][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:41:28.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:28.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:28.164][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:41:28.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:41:28.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:41:28.167][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:41:28.168][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-31 01:41:28.168][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-31 01:41:28.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:41:28.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:41:28.171][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-31 01:41:28.172][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:41:28.177][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-31 01:41:28.179][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:41:28.212][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:41:28.213][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-31 01:41:28.218][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:41:28.222][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-31 01:41:28.226][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-31 01:41:28.228][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-31 01:41:28.229][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-31 01:41:28.230][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-31 01:41:28.240][biodb::testThat]
biodb.INFO [2024-05-31 01:41:28.241][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-31 01:41:28.241][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:28.242][biodb::testThat]
biodb.TRACE[2024-05-31 01:41:28.246][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-05-31 01:41:28.248][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:41:28.252][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-31 01:41:28.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:41:28.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:41:28.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:41:28.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:41:28.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.312][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:41:28.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:41:28.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.316][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:41:28.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:41:28.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.320][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.348][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.360][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:41:28.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.364][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:41:28.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:28.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:28.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.371][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:28.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:28.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.383][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:41:28.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.387][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-31 01:41:28.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.398][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:41:28.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.477][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.489][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:41:28.515][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-31 01:41:28.518][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:41:28.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:41:28.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:41:28.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:41:28.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.525][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-31 01:41:28.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-31 01:41:28.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-31 01:41:28.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-31 01:41:28.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.563][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.594][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.598][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.602][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:28.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.623][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.624][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.626][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.649][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.650][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.652][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.663][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.694][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.698][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.699][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.701][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.702][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:28.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:28.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.716][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:28.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:28.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.720][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:28.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:28.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.723][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:28.724][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:28.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.726][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:28.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:28.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.749][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.750][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.751][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.766][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.770][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.774][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.775][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.777][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.778][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.788][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:28.789][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:28.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.791][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.794][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.795][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:28.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.797][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.801][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:28.802][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:28.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.804][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.807][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.808][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:28.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.810][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.814][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:28.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:28.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.817][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:28.820][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.821][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:28.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:28.823][ef$get] fields variable is a list.
biodb.INFO [2024-05-31 01:41:28.829][biodb::testThat]
biodb.INFO [2024-05-31 01:41:28.830][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-31 01:41:28.831][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:28.832][biodb::testThat]
biodb.DEBUG[2024-05-31 01:41:28.845][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-05-31 01:41:28.852][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:41:28.856][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.INFO [2024-05-31 01:41:28.858][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-05-31 01:41:28.859][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:41:28.860][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:41:28.861][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:41:28.862][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-31 01:41:28.863][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:41:28.864][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:41:28.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:41:28.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:28.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:28.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:28.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:28.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:28.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:41:28.879][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-05-31 01:41:28.903][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:41:28.904][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:41:28.905][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-31 01:41:30.237][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2024-05-31 01:41:30.882][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-05-31 01:41:30.885][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-05-31 01:41:30.887][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2024-05-31 01:41:30.902][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2024-05-31 01:41:30.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2024-05-31 01:41:30.906][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:41:30.930][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:41:30.932][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-31 01:41:30.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:41:30.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:30.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:30.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:30.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:30.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:30.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:41:30.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:30.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:30.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:30.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:30.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:30.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:30.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:30.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:30.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:41:30.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:41:30.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:30.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:30.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:41:30.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:41:30.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:30.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:30.965][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:41:30.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:41:30.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:30.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:30.969][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:41:30.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:41:30.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:30.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:30.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:30.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:30.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:30.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:30.993][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:30.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:41:30.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:30.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:30.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:30.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:30.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:31.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:41:31.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.006][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:41:31.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:31.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.010][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:41:31.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:31.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.014][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:31.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:31.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:41:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:41:31.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.031][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:41:31.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.035][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-31 01:41:31.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.047][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:41:31.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.072][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:31.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:31.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.076][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:31.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:31.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:31.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:31.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:31.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:41:31.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:31.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:31.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:31.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:31.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:31.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:31.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:31.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:31.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:31.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:31.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:41:31.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:41:31.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:41:31.112][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-31 01:41:31.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-31 01:41:31.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-31 01:41:31.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-31 01:41:31.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-31 01:41:31.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-31 01:41:31.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-31 01:41:31.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:41:31.132][biodb::testThat]
biodb.INFO [2024-05-31 01:41:31.133][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-31 01:41:31.134][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:31.135][biodb::testThat]
biodb.TRACE[2024-05-31 01:41:31.138][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.139][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.141][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:41:31.142][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-05-31 01:41:31.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:31.182][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:31.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:31.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:31.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:41:31.189][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-31 01:41:31.213][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-31 01:41:31.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:41:31.230][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:41:31.246][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-05-31 01:41:32.128][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-05-31 01:41:32.772][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:41:32.776][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-05-31 01:41:32.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-05-31 01:41:32.783][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-05-31 01:41:32.796][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:32.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:32.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:32.800][ef$get] fields variable is a list.
biodb.INFO [2024-05-31 01:41:32.804][biodb::testThat]
biodb.INFO [2024-05-31 01:41:32.805][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-31 01:41:32.806][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:32.807][biodb::testThat]
biodb.TRACE[2024-05-31 01:41:32.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:32.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:32.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:32.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:32.838][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:32.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:32.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:32.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:32.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:32.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:32.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:32.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:41:32.953][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-31 01:41:32.956][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:41:32.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-31 01:41:32.972][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:41:32.974][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-05-31 01:41:32.987][biodb::testThat]
biodb.INFO [2024-05-31 01:41:32.988][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-31 01:41:32.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:32.989][biodb::testThat]
biodb.TRACE[2024-05-31 01:41:33.007][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:41:33.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:41:33.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:33.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:33.011][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:41:33.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:41:33.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:33.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:33.015][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-31 01:41:33.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-31 01:41:33.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:33.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:33.018][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-31 01:41:33.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-31 01:41:33.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:33.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:33.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:41:33.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:41:33.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:33.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:33.068][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:41:33.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:41:33.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:33.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:33.071][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-31 01:41:33.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-31 01:41:33.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:33.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:33.075][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-31 01:41:33.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-31 01:41:33.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:33.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:41:33.083][biodb::testThat]
biodb.INFO [2024-05-31 01:41:33.084][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-31 01:41:33.085][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:33.086][biodb::testThat]
biodb.INFO [2024-05-31 01:41:33.093][biodb::testThat]
biodb.INFO [2024-05-31 01:41:33.094][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-31 01:41:33.095][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:33.096][biodb::testThat]
biodb.INFO [2024-05-31 01:41:33.102][biodb::testThat]
biodb.INFO [2024-05-31 01:41:33.103][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-31 01:41:33.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:33.105][biodb::testThat]
biodb.DEBUG[2024-05-31 01:41:33.108][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-05-31 01:41:33.843][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-05-31 01:41:34.285][biodb::testThat]
biodb.INFO [2024-05-31 01:41:34.287][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-31 01:41:34.289][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:34.290][biodb::testThat]
biodb.TRACE[2024-05-31 01:41:34.300][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:34.302][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:34.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.305][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.307][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.308][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.311][ef$get] fields variable is a list.
biodb.INFO [2024-05-31 01:41:34.314][biodb::testThat]
biodb.INFO [2024-05-31 01:41:34.315][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-31 01:41:34.316][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:34.317][biodb::testThat]
biodb.TRACE[2024-05-31 01:41:34.327][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:34.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:34.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:34.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:34.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.334][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:41:34.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:41:34.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:41:34.420][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-31 01:41:34.423][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:41:34.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-31 01:41:34.425][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:41:34.426][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-31 01:41:34.481][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-31 01:41:34.484][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:41:34.485][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-31 01:41:34.486][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:41:34.487][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-05-31 01:41:34.498][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-31 01:41:34.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-31 01:41:34.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:41:34.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:41:34.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:34.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:34.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:34.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:41:34.537][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-31 01:41:34.540][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:41:34.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:41:34.543][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-31 01:41:38.414][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-05-31 01:41:48.108][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:41:48.110][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-05-31 01:41:48.122][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-05-31 01:41:49.145][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-31 01:41:49.149][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:41:49.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:41:49.152][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-31 01:41:49.808][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-05-31 01:41:50.448][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:41:50.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-05-31 01:41:50.454][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-05-31 01:41:50.473][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-05-31 01:41:50.477][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:41:50.478][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:41:50.480][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-05-31 01:41:51.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-05-31 01:41:51.740][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:41:51.745][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-05-31 01:41:51.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-05-31 01:41:51.788][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-31 01:41:51.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-31 01:41:51.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:51.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:41:51.806][biodb::testThat]
biodb.INFO [2024-05-31 01:41:51.807][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-31 01:41:51.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:41:51.810][biodb::testThat]
biodb.TRACE[2024-05-31 01:41:51.814][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-31 01:41:51.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-31 01:41:51.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:51.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:51.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:41:51.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:41:51.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:51.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:51.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:51.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:51.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:51.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:51.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:51.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:51.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:51.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:51.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:51.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:41:51.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:51.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:41:51.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:41:51.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:41:51.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:41:51.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:41:51.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:41:51.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:41:51.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:41:51.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:41:51.853][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[2024-05-31 01:41:51.856][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-31 01:41:51.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:41:51.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:41:51.862][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-05-31 01:41:55.945][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-05-31 01:42:05.394][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:42:05.397][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-05-31 01:42:05.409][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-05-31 01:42:07.043][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-05-31 01:42:07.110][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-31 01:42:07.113][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-05-31 01:42:07.115][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-31 01:42:07.116][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:42:07.117][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:42:07.119][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-31 01:42:07.120][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:42:07.121][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:42:07.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:07.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:07.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:07.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:07.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:07.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:07.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:42:07.163][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-05-31 01:42:07.167][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:07.169][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:07.172][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-31 01:42:07.859][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-05-31 01:42:08.539][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:42:08.541][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-05-31 01:42:08.544][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-05-31 01:42:08.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:08.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:08.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:08.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:08.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:08.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:08.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:42:08.556][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-05-31 01:42:08.559][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:08.560][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:08.563][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-05-31 01:42:09.209][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-05-31 01:42:10.173][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:42:10.178][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-05-31 01:42:10.185][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-05-31 01:42:10.191][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-05-31 01:42:10.194][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:42:10.196][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-31 01:42:10.199][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-31 01:42:10.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:10.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:10.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:10.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:10.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:10.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:10.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:10.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:42:10.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:42:10.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:42:10.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:42:10.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.271][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:42:10.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:42:10.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.278][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:42:10.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:42:10.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.284][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:42:10.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:42:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.291][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:42:10.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:42:10.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.299][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:42:10.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:42:10.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:42:10.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:42:10.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.310][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:42:10.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.315][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:42:10.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.321][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:42:10.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:42:10.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:42:10.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:42:10.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:42:10.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:42:10.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.349][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:42:10.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.355][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-31 01:42:10.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:42:10.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:42:10.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.375][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:42:10.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.379][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.384][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.392][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:42:10.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:10.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:10.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:10.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:10.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:10.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:10.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:10.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:42:10.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:42:10.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.465][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:42:10.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:42:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.470][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:42:10.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:42:10.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.477][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:42:10.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:42:10.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.483][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:42:10.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:42:10.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:42:10.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:42:10.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.497][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:42:10.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:42:10.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.504][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:42:10.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.511][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:42:10.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:42:10.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:42:10.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:42:10.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:42:10.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:42:10.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:42:10.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.545][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:42:10.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.609][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-31 01:42:10.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:42:10.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:42:10.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.625][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:42:10.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:42:10.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.630][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.634][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.643][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:10.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:10.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:42:10.700][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-05-31 01:42:10.719][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:42:10.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:10.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:10.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:10.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:10.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:10.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:10.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:10.734][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.743][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.744][private$selectFields]
biodb.TRACE[2024-05-31 01:42:10.745][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:10.746][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:10.747][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.748][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.749][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.751][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.752][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.754][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.756][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.758][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.760][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.761][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.763][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.766][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.768][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:10.770][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.777][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.784][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.811][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-31 01:42:10.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:10.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:10.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:10.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:10.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:10.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:10.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:10.832][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.838][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.844][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.846][private$selectFields]
biodb.TRACE[2024-05-31 01:42:10.848][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:10.849][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:10.851][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.853][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.855][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.859][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.861][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.862][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.865][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.866][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.867][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.868][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.869][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.871][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.872][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:10.873][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.878][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.882][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.887][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-31 01:42:10.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:10.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:10.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:10.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:10.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:10.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:10.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:10.900][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.904][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.909][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.910][private$selectFields]
biodb.TRACE[2024-05-31 01:42:10.911][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:10.912][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:10.913][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.914][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.915][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.917][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.918][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.919][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.921][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.922][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.923][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:10.924][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.925][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.927][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.928][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:10.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.934][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.938][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:10.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.942][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-31 01:42:10.943][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:42:10.944][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:42:10.955][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-31 01:42:10.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-31 01:42:10.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:42:10.963][biodb::testThat]
biodb.INFO [2024-05-31 01:42:10.964][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-31 01:42:10.965][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:42:10.966][biodb::testThat]
biodb.TRACE[2024-05-31 01:42:10.971][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-31 01:42:10.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-31 01:42:10.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:42:10.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:42:10.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:10.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:10.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:10.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:42:11.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:11.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:11.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:11.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:11.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:11.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:11.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:42:11.086][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-05-31 01:42:11.089][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:11.090][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:11.092][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-05-31 01:42:15.135][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-05-31 01:42:24.992][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:42:25.002][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-05-31 01:42:25.026][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-05-31 01:42:26.808][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:42:26.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:26.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:26.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:26.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:26.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:26.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:26.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:26.881][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:26.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:26.889][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:26.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:26.930][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:26.932][private$selectFields]
biodb.TRACE[2024-05-31 01:42:26.934][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:26.936][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:26.938][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:26.940][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.942][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:26.946][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:26.948][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.949][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:26.952][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:26.954][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:26.973][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:26.975][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.977][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:26.981][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:26.983][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:26.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:26.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:26.992][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:26.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:26.999][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.006][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-31 01:42:27.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:27.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:27.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:27.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:27.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:27.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:27.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:27.025][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.030][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.036][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:27.038][private$selectFields]
biodb.TRACE[2024-05-31 01:42:27.039][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:27.040][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:27.041][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:27.042][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.044][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.049][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.050][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.053][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.055][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:27.056][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:27.058][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.060][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.063][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.064][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:27.066][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.073][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.077][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.081][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-31 01:42:27.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:27.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:27.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:27.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:27.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:27.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:27.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:27.098][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.105][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.112][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:27.114][private$selectFields]
biodb.TRACE[2024-05-31 01:42:27.126][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:27.129][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:27.130][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:27.132][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.133][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.136][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.137][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.138][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.141][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.143][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:27.145][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:27.146][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.148][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.152][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.154][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:27.156][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.164][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.170][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:27.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.179][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-31 01:42:27.181][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:42:27.183][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:42:27.196][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-31 01:42:27.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-31 01:42:27.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:42:27.207][biodb::testThat]
biodb.INFO [2024-05-31 01:42:27.209][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-31 01:42:27.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:42:27.211][biodb::testThat]
biodb.TRACE[2024-05-31 01:42:27.215][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-31 01:42:27.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-31 01:42:27.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:42:27.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:42:27.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:27.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:27.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:27.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:27.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:27.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:27.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:27.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:42:27.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:27.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:42:27.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:27.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:27.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:27.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:27.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:27.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:27.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:42:27.284][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-31 01:42:27.291][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:42:27.294][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-31 01:42:27.297][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:42:27.372][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-31 01:42:29.183][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:42:29.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:29.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:29.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:29.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:29.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:29.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:29.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:29.206][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.213][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.220][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.221][private$selectFields]
biodb.TRACE[2024-05-31 01:42:29.223][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:29.224][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:29.226][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.228][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.230][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.233][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.234][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.236][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.238][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.239][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.240][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.241][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.242][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.244][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.245][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:29.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.252][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.259][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.266][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-31 01:42:29.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:29.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:29.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:29.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:29.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:29.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:29.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:29.280][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.293][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.295][private$selectFields]
biodb.TRACE[2024-05-31 01:42:29.296][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:29.298][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:29.299][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.301][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.303][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.306][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.308][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.309][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.312][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.314][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.315][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.317][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.318][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.321][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.323][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:29.325][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.332][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.339][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.346][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-31 01:42:29.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:29.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:29.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:29.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:29.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:29.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:29.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:29.365][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.377][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.378][private$selectFields]
biodb.TRACE[2024-05-31 01:42:29.379][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:42:29.380][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:42:29.381][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.383][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.385][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.388][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.390][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.391][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.394][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.396][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.398][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:42:29.399][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.401][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.405][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.407][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-31 01:42:29.408][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.415][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.420][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:29.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:29.426][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-31 01:42:29.427][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:42:29.429][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:42:29.459][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-31 01:42:29.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-31 01:42:29.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:29.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:42:29.473][biodb::testThat]
biodb.INFO [2024-05-31 01:42:29.475][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-31 01:42:29.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:42:29.479][biodb::testThat]
biodb.DEBUG[2024-05-31 01:42:29.482][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-31 01:42:29.485][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:42:29.488][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-31 01:42:29.491][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:42:29.493][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:42:29.495][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:42:29.497][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-31 01:42:29.499][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:42:29.501][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:42:29.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:29.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:29.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:29.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:29.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:29.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:29.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:42:29.526][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-05-31 01:42:29.531][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:29.533][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:29.536][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:30.242][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:30.245][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:30.247][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:30.250][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:31.034][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:31.037][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:31.039][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:31.042][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:31.682][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:31.683][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:31.684][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:31.685][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:32.460][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:32.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:32.465][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:32.467][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:33.114][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:33.116][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:33.118][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:33.120][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:33.898][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:33.900][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:33.902][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:33.905][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:34.546][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:34.548][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:34.549][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:34.550][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:35.321][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:35.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:35.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:35.329][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:35.980][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:35.982][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:35.983][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:35.984][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:36.767][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:36.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:36.771][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:36.772][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:37.403][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:37.406][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:37.408][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:37.410][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:38.200][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:38.202][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:38.203][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:38.204][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:38.842][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:38.843][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:38.844][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:38.845][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:39.615][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:39.619][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:39.622][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:39.625][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:40.195][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:40.196][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:40.197][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:40.198][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:40.943][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:40.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:40.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:40.947][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:41.520][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:41.523][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:41.525][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:41.528][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:42.322][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:42.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:42.327][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:42.330][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-31 01:42:42.899][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:42.900][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:42.902][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:42.904][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-31 01:42:43.655][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-31 01:42:43.663][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-05-31 01:42:43.667][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:42:43.670][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:42:43.673][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-31 01:42:43.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:43.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:43.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:43.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:43.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:43.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:43.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:42:43.705][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:43.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:43.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:43.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:43.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:43.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:42:43.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:43.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:43.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:43.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:43.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:43.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:43.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:43.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:43.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:43.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:43.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:43.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:43.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:43.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:43.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:43.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:43.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:43.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:43.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:43.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:43.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:43.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:42:43.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:42:43.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:42:43.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:42:43.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:42:43.748][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-31 01:42:43.749][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-31 01:42:43.757][biodb::testThat]
biodb.INFO [2024-05-31 01:42:43.758][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-31 01:42:43.813][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:42:43.814][biodb::testThat]
biodb.DEBUG[2024-05-31 01:42:43.821][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-05-31 01:42:43.822][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-05-31 01:42:43.823][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-31 01:42:43.825][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-05-31 01:42:43.826][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-31 01:42:43.827][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:42:43.829][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:42:43.830][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-31 01:42:43.831][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:42:43.832][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:42:43.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:43.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:43.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:43.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:43.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:43.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:43.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:42:43.845][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-05-31 01:42:43.848][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:43.849][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:43.850][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:44.429][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:44.430][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:44.431][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:44.432][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:45.125][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:45.126][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:45.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:45.129][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:45.724][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:45.726][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:45.727][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:45.728][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:46.421][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:46.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:46.426][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:46.429][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:47.005][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:47.007][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:47.008][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:47.009][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:47.701][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:47.702][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:47.703][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:47.705][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:48.263][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:48.264][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:48.265][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:48.266][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:48.959][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:48.962][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:48.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:48.967][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:49.570][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:49.571][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:49.572][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:49.573][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:50.325][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:50.327][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:50.330][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:50.333][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:50.905][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:50.906][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:50.907][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:50.908][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:51.653][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:51.654][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:51.655][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:51.657][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:52.216][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:52.218][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:52.219][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:52.220][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:53.013][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:53.016][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:53.018][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:53.021][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:53.627][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:53.628][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:53.629][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:53.630][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:54.375][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:54.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:54.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:54.379][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:54.929][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:54.931][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:54.932][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:54.933][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:55.720][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:55.722][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:55.723][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:55.724][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-31 01:42:56.285][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:56.286][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:56.287][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:56.289][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-31 01:42:57.082][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:57.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:42:57.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:42:57.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:42:57.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:42:57.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:42:57.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:42:57.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:42:57.114][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-05-31 01:42:57.122][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:57.125][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:57.128][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:42:57.737][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:57.739][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:57.740][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:57.742][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:42:58.536][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:58.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:58.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:58.544][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:42:59.148][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:42:59.150][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:42:59.151][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:42:59.152][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:42:59.846][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:42:59.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:42:59.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:42:59.849][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:43:00.408][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:43:00.410][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:43:00.411][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:43:00.412][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:43:01.105][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:43:01.108][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:01.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:01.114][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:43:01.718][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:43:01.719][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:43:01.721][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:43:01.722][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:43:02.423][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:43:02.427][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:02.429][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:02.433][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:43:03.031][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:43:03.033][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:43:03.034][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:43:03.035][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:43:03.782][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:43:03.784][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:03.786][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:03.789][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:43:04.384][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:43:04.386][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:43:04.387][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:43:04.388][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:43:05.133][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:43:05.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:05.136][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:05.137][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:43:05.694][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:43:05.696][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:43:05.697][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:43:05.698][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:43:06.445][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:43:06.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:06.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:06.448][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:43:07.006][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:43:07.009][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:43:07.011][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:43:07.012][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:43:07.704][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:43:07.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:07.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:07.708][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:43:08.269][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:43:08.272][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:43:08.275][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:43:08.278][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:43:09.070][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-31 01:43:09.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:09.075][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:09.078][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-31 01:43:09.679][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-31 01:43:09.682][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-31 01:43:09.684][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-31 01:43:09.687][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-31 01:43:10.485][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-31 01:43:10.494][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-05-31 01:43:10.498][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:43:10.501][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-31 01:43:10.504][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-31 01:43:10.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:43:10.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:10.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:10.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:10.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:10.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:10.532][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.TRACE[2024-05-31 01:43:10.536][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:10.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:10.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.543][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:10.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:10.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:43:10.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:43:10.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:10.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:10.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:10.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:10.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:10.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:43:10.567][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:10.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:10.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.572][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:10.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:10.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:10.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:10.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:10.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:10.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:43:10.620][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-31 01:43:10.622][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-31 01:43:10.623][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-05-31 01:43:10.831][biodb::testThat]
biodb.INFO [2024-05-31 01:43:10.832][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-31 01:43:10.833][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:43:10.834][biodb::testThat]
biodb.INFO [2024-05-31 01:43:10.874][biodb::testThat]
biodb.INFO [2024-05-31 01:43:10.875][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-31 01:43:10.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:43:10.877][biodb::testThat]
biodb.INFO [2024-05-31 01:43:10.884][biodb::testThat]
biodb.INFO [2024-05-31 01:43:10.885][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-31 01:43:10.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:43:10.887][biodb::testThat]
biodb.DEBUG[2024-05-31 01:43:10.890][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-31 01:43:10.893][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:10.894][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:10.896][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-05-31 01:43:15.040][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-05-31 01:43:24.568][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:43:24.571][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-05-31 01:43:24.581][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-05-31 01:43:25.474][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:25.476][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:25.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:25.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:25.479][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:25.480][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:25.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:25.482][ef$get] fields variable is a list.
biodb.INFO [2024-05-31 01:43:25.484][biodb::testThat]
biodb.INFO [2024-05-31 01:43:25.485][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-31 01:43:25.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:43:25.487][biodb::testThat]
biodb.ERROR[2024-05-31 01:43:25.502][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-31 01:43:25.520][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-31 01:43:25.533][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-31 01:43:25.535][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-31 01:43:25.536][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-31 01:43:25.537][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-31 01:43:25.538][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:25.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:25.540][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.541][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-31 01:43:25.553][biodb::testContext]
biodb.INFO [2024-05-31 01:43:25.554][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:43:25.555][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-05-31 01:43:25.555][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:43:25.556][biodb::testContext]
biodb.INFO [2024-05-31 01:43:25.559][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-31 01:43:25.560][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-31 01:43:25.564][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:43:25.565][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-31 01:43:25.566][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-31 01:43:25.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.570][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-31 01:43:25.571][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-31 01:43:25.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.575][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-31 01:43:25.576][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-31 01:43:25.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.579][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-31 01:43:25.580][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-31 01:43:25.582][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-31 01:43:25.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.585][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-31 01:43:25.586][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-31 01:43:25.587][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-31 01:43:25.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.591][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-31 01:43:25.592][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-31 01:43:25.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.595][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-31 01:43:25.596][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-31 01:43:25.597][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-31 01:43:25.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.601][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-31 01:43:25.602][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-31 01:43:25.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.606][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-31 01:43:25.607][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-31 01:43:25.608][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-31 01:43:25.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.611][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:43:25.612][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-31 01:43:25.613][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-31 01:43:25.614][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-31 01:43:25.615][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-31 01:43:25.616][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-31 01:43:25.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.620][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-31 01:43:25.621][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-31 01:43:25.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.625][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-31 01:43:25.626][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-31 01:43:25.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.630][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-31 01:43:25.631][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-31 01:43:25.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.634][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[2024-05-31 01:43:25.635][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-31 01:43:25.636][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-31 01:43:25.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.640][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-31 01:43:25.641][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-31 01:43:25.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.644][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:43:25.645][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-31 01:43:25.649][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-31 01:43:25.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.653][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-31 01:43:25.654][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-31 01:43:25.655][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-31 01:43:25.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.659][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-31 01:43:25.661][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.662][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-31 01:43:25.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:25.665][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.666][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.667][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.668][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.669][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:43:25.670][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:25.671][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.672][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-31 01:43:25.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:25.674][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.676][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:43:25.676][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:43:25.676][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:43:25.676][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:43:25.676][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:43:25.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:25.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:25.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:25.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:25.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:25.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:25.683][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.684][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.685][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:25.686][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:25.687][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.688][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.689][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-31 01:43:25.691][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.692][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:43:25.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.694][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:25.695][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.696][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.697][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.698][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.699][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:43:25.700][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:25.701][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.702][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-31 01:43:25.703][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:25.704][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.705][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.706][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:43:25.706][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:43:25.706][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:43:25.706][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:43:25.706][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:43:25.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:25.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:25.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:25.710][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:25.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:25.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:25.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.714][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.715][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:25.716][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:25.717][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.718][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.719][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-31 01:43:25.721][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.722][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-31 01:43:25.723][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.724][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:25.725][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.726][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.727][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.729][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:43:25.730][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:25.731][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.732][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-31 01:43:25.733][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:25.734][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.735][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.736][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.737][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:25.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:25.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:25.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:25.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:25.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:25.743][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.744][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:25.746][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:25.747][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.748][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.749][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-31 01:43:25.751][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.752][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:43:25.753][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.754][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:25.755][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.756][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.757][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.758][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.759][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:43:25.760][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:25.761][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.762][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-31 01:43:25.763][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:25.764][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.765][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:25.766][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.767][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:25.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:25.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:25.770][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:25.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:25.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:25.773][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:25.774][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.775][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:25.776][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:25.777][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:25.778][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:25.779][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:43:25.780][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.879][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[2024-05-31 01:43:25.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:25.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:25.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:25.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:25.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:25.904][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-31 01:43:25.906][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-31 01:43:25.907][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-31 01:43:25.908][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-31 01:43:25.910][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:43:25.911][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-31 01:43:25.914][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-31 01:43:25.915][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-31 01:43:25.916][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-31 01:43:25.918][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-31 01:43:25.919][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:43:25.920][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-31 01:43:25.922][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-31 01:43:25.923][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-31 01:43:25.924][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-31 01:43:25.926][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:43:25.927][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-31 01:43:25.928][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-31 01:43:25.930][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:43:25.931][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-31 01:43:25.932][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-31 01:43:25.933][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-31 01:43:25.935][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-31 01:43:25.936][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-31 01:43:25.937][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-31 01:43:25.938][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-31 01:43:25.940][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-31 01:43:25.941][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-31 01:43:25.942][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-31 01:43:25.944][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-31 01:43:25.945][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-31 01:43:25.946][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-31 01:43:25.947][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-31 01:43:25.949][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-31 01:43:25.950][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-31 01:43:25.951][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-31 01:43:25.953][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-31 01:43:25.954][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-31 01:43:25.955][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-31 01:43:25.956][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-31 01:43:25.958][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-31 01:43:25.959][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-31 01:43:25.960][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-31 01:43:25.962][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-31 01:43:25.963][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-31 01:43:25.964][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-31 01:43:25.965][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-31 01:43:25.967][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-31 01:43:25.968][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-31 01:43:25.969][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-31 01:43:25.971][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-31 01:43:25.972][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-31 01:43:25.973][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-31 01:43:25.974][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-31 01:43:25.976][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-31 01:43:25.977][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-31 01:43:25.978][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-31 01:43:25.980][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-31 01:43:25.981][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-31 01:43:25.982][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-31 01:43:25.984][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-31 01:43:25.985][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-31 01:43:25.986][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-31 01:43:25.988][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-31 01:43:25.989][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-31 01:43:25.991][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-31 01:43:25.992][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:43:25.994][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:43:25.995][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-31 01:43:25.996][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-31 01:43:25.998][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-31 01:43:25.999][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-31 01:43:26.000][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-31 01:43:26.002][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-31 01:43:26.003][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-31 01:43:26.005][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-31 01:43:26.006][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-31 01:43:26.007][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-31 01:43:26.009][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-31 01:43:26.010][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-31 01:43:26.011][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-31 01:43:26.013][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-31 01:43:26.014][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-31 01:43:26.016][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-31 01:43:26.017][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-31 01:43:26.018][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:43:26.019][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.021][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:26.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:26.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:26.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:26.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:26.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:26.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:26.127][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-31 01:43:26.129][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:43:26.131][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:26.132][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-31 01:43:26.133][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:26.134][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:26.135][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:26.136][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:26.137][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:26.138][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:26.139][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:43:26.140][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:26.141][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:26.142][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-31 01:43:26.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-31 01:43:26.144][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-31 01:43:26.145][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:26.146][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:43:26.146][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:43:26.147][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:26.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:26.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:26.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:26.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:26.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:26.162][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:26.163][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-31 01:43:26.163][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-31 01:43:26.164][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:26.165][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:26.166][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:26.167][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:26.168][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-31 01:43:26.169][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:43:26.173][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:43:26.174][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-31 01:43:26.175][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:43:26.176][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-31 01:43:26.177][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-31 01:43:26.178][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-31 01:43:26.180][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-31 01:43:26.181][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-31 01:43:26.182][biodb::testThat]
biodb.INFO [2024-05-31 01:43:26.183][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-05-31 01:43:26.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:43:26.185][biodb::testThat]
biodb.DEBUG[2024-05-31 01:43:26.188][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-05-31 01:43:26.192][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:26.193][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:26.195][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-05-31 01:43:26.822][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-05-31 01:43:27.478][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:43:27.482][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-05-31 01:43:27.490][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-05-31 01:43:27.508][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-05-31 01:43:27.536][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:27.538][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:27.540][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-05-31 01:43:28.182][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-05-31 01:43:28.843][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:43:28.849][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-05-31 01:43:28.858][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-05-31 01:43:28.883][biodb::testThat]
biodb.INFO [2024-05-31 01:43:28.885][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-05-31 01:43:28.887][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:43:28.889][biodb::testThat]
biodb.INFO [2024-05-31 01:43:28.928][biodb::testThat]
biodb.INFO [2024-05-31 01:43:28.930][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-05-31 01:43:28.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:43:28.932][biodb::testThat]
biodb.DEBUG[2024-05-31 01:43:28.935][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-31 01:43:28.938][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:28.939][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:28.941][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-05-31 01:43:29.410][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-05-31 01:43:29.885][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:43:29.887][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-05-31 01:43:29.891][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-05-31 01:43:29.897][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-31 01:43:29.900][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:43:29.901][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-31 01:43:29.903][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:43:29.904][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-31 01:43:29.911][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-05-31 01:43:29.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:29.915][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-31 01:43:29.916][rule$waitAsNeeded] Wait 0.0243106 second(s).
biodb.TRACE[2024-05-31 01:43:29.942][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-05-31 01:43:30.413][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-05-31 01:43:30.884][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:43:30.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-05-31 01:43:30.898][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-05-31 01:43:30.915][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-05-31 01:43:30.922][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:30.925][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-31 01:43:30.928][rule$waitAsNeeded] Wait 0.0148294 second(s).
biodb.TRACE[2024-05-31 01:43:30.946][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-05-31 01:43:32.173][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-05-31 01:43:35.447][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:43:35.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-05-31 01:43:35.455][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-05-31 01:43:35.594][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-05-31 01:43:35.598][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:43:35.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:43:35.602][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-05-31 01:43:36.852][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-05-31 01:43:40.105][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:43:40.108][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-05-31 01:43:40.114][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-05-31 01:43:40.253][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-31 01:43:40.255][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-31 01:43:40.257][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-31 01:43:40.258][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-31 01:43:40.259][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.261][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.263][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-31 01:43:40.269][biodb::testContext]
biodb.INFO [2024-05-31 01:43:40.270][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:43:40.271][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-05-31 01:43:40.272][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:43:40.273][biodb::testContext]
biodb.INFO [2024-05-31 01:43:40.276][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-31 01:43:40.278][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-31 01:43:40.282][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:43:40.283][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-31 01:43:40.285][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-31 01:43:40.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.289][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-31 01:43:40.290][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-31 01:43:40.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.294][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-31 01:43:40.295][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-31 01:43:40.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.299][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-31 01:43:40.300][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-31 01:43:40.302][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-31 01:43:40.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.306][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-31 01:43:40.307][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-31 01:43:40.308][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-31 01:43:40.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.312][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-31 01:43:40.313][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-31 01:43:40.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.319][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-31 01:43:40.320][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-31 01:43:40.321][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-31 01:43:40.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.326][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-31 01:43:40.327][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-31 01:43:40.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.331][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-31 01:43:40.332][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-31 01:43:40.333][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-31 01:43:40.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.337][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:43:40.338][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-31 01:43:40.339][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-31 01:43:40.340][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-31 01:43:40.342][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-31 01:43:40.343][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-31 01:43:40.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.348][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-31 01:43:40.349][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-31 01:43:40.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.353][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-31 01:43:40.354][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-31 01:43:40.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.357][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-31 01:43:40.359][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-31 01:43:40.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.411][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-31 01:43:40.412][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-31 01:43:40.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.416][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-31 01:43:40.417][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-31 01:43:40.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.421][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:43:40.422][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-31 01:43:40.427][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-31 01:43:40.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.430][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-31 01:43:40.431][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-31 01:43:40.432][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-31 01:43:40.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.436][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-31 01:43:40.438][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.439][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-31 01:43:40.440][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.441][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:40.442][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.443][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.444][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.446][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.447][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:43:40.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:40.449][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.450][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-31 01:43:40.451][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:40.452][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.453][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.454][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:43:40.454][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:43:40.454][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:43:40.454][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:43:40.454][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:43:40.455][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:40.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.458][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:40.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.461][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.462][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.463][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:40.464][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:40.465][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.466][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.467][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-31 01:43:40.469][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.470][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:43:40.471][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.472][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:40.473][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.474][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.475][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.476][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.477][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:43:40.478][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:40.479][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.480][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-31 01:43:40.481][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:40.482][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.483][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.484][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:43:40.484][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:43:40.484][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:43:40.484][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:43:40.484][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:43:40.485][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:40.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.487][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:40.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.490][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.491][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.492][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:40.493][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:40.494][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.495][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.496][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-31 01:43:40.498][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.499][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-31 01:43:40.500][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.501][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:40.502][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.503][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.504][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.505][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.506][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:43:40.507][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:40.508][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.509][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-31 01:43:40.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:40.511][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.512][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.513][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.514][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:40.515][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.517][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:40.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.520][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.521][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:40.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:40.523][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.524][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.526][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-31 01:43:40.527][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.528][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:43:40.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:40.531][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.532][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.534][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.536][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:43:40.537][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:40.538][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.539][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-31 01:43:40.540][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:40.541][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.542][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.543][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.544][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:40.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.546][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:40.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.549][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.550][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.551][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:40.552][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:40.553][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.554][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.556][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:43:40.556][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.621][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[2024-05-31 01:43:40.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.634][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[2024-05-31 01:43:40.635][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-31 01:43:40.637][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-31 01:43:40.638][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-31 01:43:40.640][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-31 01:43:40.641][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:43:40.642][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-31 01:43:40.644][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-31 01:43:40.645][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-31 01:43:40.646][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-31 01:43:40.648][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-31 01:43:40.650][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:43:40.651][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-31 01:43:40.653][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-31 01:43:40.654][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-31 01:43:40.655][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-31 01:43:40.657][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:43:40.658][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-31 01:43:40.659][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-31 01:43:40.661][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:43:40.662][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-31 01:43:40.663][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-31 01:43:40.665][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-31 01:43:40.666][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-31 01:43:40.667][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-31 01:43:40.669][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-31 01:43:40.670][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-31 01:43:40.671][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-31 01:43:40.673][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-31 01:43:40.674][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-31 01:43:40.675][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-31 01:43:40.677][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-31 01:43:40.678][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-31 01:43:40.679][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-31 01:43:40.681][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-31 01:43:40.682][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-31 01:43:40.683][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-31 01:43:40.685][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-31 01:43:40.686][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-31 01:43:40.687][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-31 01:43:40.689][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-31 01:43:40.690][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-31 01:43:40.691][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-31 01:43:40.692][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-31 01:43:40.694][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-31 01:43:40.695][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-31 01:43:40.696][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-31 01:43:40.698][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-31 01:43:40.699][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-31 01:43:40.701][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-31 01:43:40.702][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-31 01:43:40.703][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-31 01:43:40.705][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-31 01:43:40.706][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-31 01:43:40.707][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-31 01:43:40.709][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-31 01:43:40.710][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-31 01:43:40.711][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-31 01:43:40.712][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-31 01:43:40.714][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-31 01:43:40.715][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-31 01:43:40.716][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-31 01:43:40.718][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-31 01:43:40.719][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-31 01:43:40.720][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-31 01:43:40.722][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-31 01:43:40.723][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-31 01:43:40.734][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:43:40.736][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:43:40.737][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-31 01:43:40.739][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-31 01:43:40.740][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-31 01:43:40.741][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-31 01:43:40.742][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-31 01:43:40.744][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-31 01:43:40.745][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-31 01:43:40.746][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-31 01:43:40.747][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-31 01:43:40.749][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-31 01:43:40.750][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-31 01:43:40.751][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-31 01:43:40.753][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-31 01:43:40.754][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-31 01:43:40.755][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-31 01:43:40.756][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-31 01:43:40.758][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-31 01:43:40.759][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:43:40.760][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.761][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.826][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[2024-05-31 01:43:40.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:43:40.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:43:40.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:40.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:40.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:40.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:40.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:40.860][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[2024-05-31 01:43:40.862][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-31 01:43:40.863][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:43:40.865][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.866][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.867][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.868][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:43:40.869][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.870][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.871][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.872][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.873][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:43:40.874][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:43:40.875][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.876][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-31 01:43:40.877][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-31 01:43:40.879][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-31 01:43:40.879][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:43:40.879][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:43:40.880][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:43:40.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:43:40.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:43:40.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:43:40.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:43:40.887][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-31 01:43:40.887][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-31 01:43:40.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:43:40.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:43:40.889][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-31 01:43:40.890][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:43:40.892][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-31 01:43:40.893][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:43:40.896][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:43:40.897][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-31 01:43:40.898][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-31 01:43:40.900][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-31 01:43:40.901][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-31 01:43:40.902][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-31 01:43:40.903][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-31 01:43:40.904][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-31 01:43:40.905][biodb::testThat]
biodb.INFO [2024-05-31 01:43:40.906][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-05-31 01:43:40.907][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:43:40.908][biodb::testThat]
biodb.DEBUG[2024-05-31 01:43:40.912][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-31 01:43:40.916][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:43:40.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-31 01:43:40.918][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:43:40.967][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-05-31 01:43:41.874][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-05-31 01:43:41.876][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-31 01:43:41.878][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-05-31 01:43:41.879][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-31 01:43:41.881][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-05-31 01:43:41.882][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:43:41.883][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-31 01:43:41.884][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-31 01:43:41.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:43:41.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:41.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:41.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:41.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:41.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:41.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:43:41.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:41.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:41.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:41.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:41.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:41.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:41.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:41.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:41.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.956][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:43:41.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:43:41.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.961][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:43:41.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:43:41.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:41.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:41.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.969][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:41.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:41.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.973][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:41.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:41.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.977][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:41.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:41.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.981][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:43:41.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:41.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.985][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:43:41.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:41.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.990][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:41.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:41.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.994][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:41.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:41.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:41.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:41.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:41.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.006][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:43:42.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.010][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-31 01:43:42.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.023][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:43:42.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.047][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.051][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:43:42.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:43:42.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:42.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:42.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:42.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:42.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:42.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:43:42.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.106][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:43:42.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-31 01:43:42.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.110][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:43:42.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:43:42.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.114][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.118][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.131][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:43:42.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.135][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-31 01:43:42.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.139][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.143][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.156][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:43:42.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.160][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-31 01:43:42.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.172][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-31 01:43:42.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.176][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.180][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.202][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:43:42.240][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-05-31 01:43:42.242][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:43:42.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:43:42.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:42.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:42.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:42.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:42.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:42.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:43:42.254][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:43:42.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:43:42.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.257][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:43:42.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:43:42.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.261][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-31 01:43:42.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-31 01:43:42.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.265][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-31 01:43:42.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-31 01:43:42.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.268][private$selectFields] Fields none
biodb.TRACE[2024-05-31 01:43:42.269][private$selectFields]
biodb.TRACE[2024-05-31 01:43:42.270][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-31 01:43:42.271][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:43:42.272][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:43:42.273][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.274][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.276][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.276][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.279][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.280][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.281][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.283][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.284][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.285][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.286][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.287][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.288][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.290][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.291][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.292][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.294][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.295][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.296][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.297][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.298][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.299][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.301][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.302][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.303][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.305][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.306][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.308][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.309][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.310][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.312][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.313][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.314][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.315][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.316][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.317][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.319][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.320][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.321][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.323][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.324][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.330][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.333][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.335][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.337][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.339][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:43:42.340][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:43:42.341][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.342][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.346][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.347][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.349][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.350][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.351][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.353][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.354][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.355][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.357][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.358][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.359][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.361][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.363][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.364][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.366][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.367][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.368][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.370][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.371][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.372][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.374][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.375][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-05-31 01:43:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.410][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.419][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.439][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.464][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.468][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.472][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.484][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-05-31 01:43:42.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:43:42.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:42.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:42.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:42.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:42.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:42.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:43:42.499][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:43:42.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:43:42.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.503][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:43:42.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:43:42.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.507][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-31 01:43:42.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-31 01:43:42.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.511][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-31 01:43:42.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-31 01:43:42.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.542][private$selectFields] Fields none
biodb.TRACE[2024-05-31 01:43:42.543][private$selectFields]
biodb.TRACE[2024-05-31 01:43:42.544][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-31 01:43:42.545][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:43:42.546][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:43:42.547][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.548][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.550][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.551][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.552][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.553][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.554][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.555][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.557][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.558][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.559][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.561][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.562][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.563][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.565][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.566][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.567][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.569][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.570][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.571][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.573][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.574][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.575][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.577][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.578][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.579][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.581][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.582][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.583][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.585][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.586][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.587][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.589][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.590][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.591][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.592][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.593][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.594][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.596][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.597][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.598][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.600][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.601][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.602][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.604][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.605][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.606][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.608][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.609][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:43:42.610][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-31 01:43:42.611][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.612][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.614][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.615][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.618][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.619][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.620][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.622][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.623][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.624][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.626][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.627][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.628][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.630][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.631][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.632][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.633][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.634][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.636][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.637][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.638][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.639][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.641][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.642][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-05-31 01:43:42.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:43:42.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:43:42.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:43:42.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.668][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.672][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.676][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-31 01:43:42.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.680][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.684][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-31 01:43:42.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:43:42.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.707][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:43:42.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:43:42.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:43:42.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:43:42.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.726][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.730][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.733][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-31 01:43:42.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:43:42.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:43:42.741][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-05-31 01:43:42.742][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:43:42.742][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-05-31 01:43:42.747][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-31 01:43:42.749][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-31 01:43:42.750][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-31 01:43:42.751][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-31 01:43:42.751][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:43:42.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:43:42.753][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:43:42.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:43:42.755][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:43:42.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]

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

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

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

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn0.6160.0840.700
LipidmapsStructureEntry0.1310.0000.131