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This page was generated on 2024-06-07 20:25 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on palomino3

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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-06-06 01:03:47 -0400 (Thu, 06 Jun 2024)
EndedAt: 2024-06-06 01:11:14 -0400 (Thu, 06 Jun 2024)
EllapsedTime: 447.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biodbLipidmaps/DESCRIPTION' ... OK
* this is package 'biodbLipidmaps' version '1.10.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'biodbLipidmaps' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
LipidmapsStructureConn 3.96   2.45  157.91
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-06-06 01:09:07.385][biodb::testContext]
biodb.INFO [2024-06-06 01:09:07.390][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-06 01:09:07.392][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-06 01:09:07.393][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-06 01:09:07.395][biodb::testContext]
biodb.INFO [2024-06-06 01:09:07.405][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-06 01:09:07.411][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-06 01:09:07.423][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:09:07.425][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-06 01:09:07.427][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-06 01:09:07.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.432][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-06 01:09:07.469][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-06 01:09:07.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.477][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-06 01:09:07.479][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-06 01:09:07.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.484][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-06 01:09:07.485][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-06 01:09:07.486][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-06 01:09:07.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.491][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-06 01:09:07.492][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-06 01:09:07.494][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-06 01:09:07.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.501][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-06 01:09:07.502][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-06 01:09:07.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.507][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-06 01:09:07.508][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-06 01:09:07.510][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-06 01:09:07.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.516][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-06 01:09:07.518][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-06 01:09:07.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.522][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-06 01:09:07.524][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-06 01:09:07.525][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-06 01:09:07.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.530][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-06 01:09:07.532][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-06 01:09:07.534][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-06 01:09:07.536][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-06 01:09:07.538][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-06 01:09:07.541][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-06 01:09:07.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.548][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-06 01:09:07.550][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-06 01:09:07.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.559][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-06 01:09:07.561][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-06 01:09:07.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.567][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[2024-06-06 01:09:07.569][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-06 01:09:07.571][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-06 01:09:07.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.578][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-06 01:09:07.581][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-06 01:09:07.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.588][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-06 01:09:07.591][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-06 01:09:07.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.595][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-06 01:09:07.597][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-06 01:09:07.602][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-06 01:09:07.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.608][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-06 01:09:07.609][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-06 01:09:07.610][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-06 01:09:07.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.618][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-06 01:09:07.660][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.684][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-06 01:09:07.686][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:09:07.689][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.690][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.691][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.693][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.694][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:09:07.696][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:09:07.697][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.698][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-06 01:09:07.700][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:09:07.701][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.702][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.704][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:09:07.704][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:09:07.704][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-06 01:09:07.704][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-06 01:09:07.704][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-06 01:09:07.705][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:09:07.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:07.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:07.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:09:07.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:07.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:07.719][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.720][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.721][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:09:07.722][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:09:07.723][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.725][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.726][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-06 01:09:07.728][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.729][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-06 01:09:07.731][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.732][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:09:07.733][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.734][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.735][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.737][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.738][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-06 01:09:07.739][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:09:07.740][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.742][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-06 01:09:07.743][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:09:07.744][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.745][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.746][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:09:07.746][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:09:07.746][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-06 01:09:07.746][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-06 01:09:07.746][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-06 01:09:07.748][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:09:07.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:07.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:07.751][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:09:07.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:07.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:07.755][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.756][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.757][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:09:07.758][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:09:07.759][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.761][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.763][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-06 01:09:07.765][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.766][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-06 01:09:07.767][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.768][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:09:07.770][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.771][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.772][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.773][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.775][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:09:07.776][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:09:07.777][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.779][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-06 01:09:07.780][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:09:07.781][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.782][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.783][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.785][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:09:07.786][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:07.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:07.788][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:09:07.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:07.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:07.792][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.793][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.794][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:09:07.795][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:09:07.797][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.798][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.800][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-06 01:09:07.802][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.803][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-06 01:09:07.804][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.805][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:09:07.807][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.812][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-06 01:09:07.813][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:09:07.814][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.815][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-06 01:09:07.817][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:09:07.818][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.819][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:07.820][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.822][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:09:07.823][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:07.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:07.825][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:09:07.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:07.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:07.831][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:09:07.832][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.833][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:09:07.835][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:09:07.837][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:07.839][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:07.843][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:09:07.845][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.847][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[2024-06-06 01:09:07.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.896][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.DEBUG[2024-06-06 01:09:07.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:07.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:07.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:07.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:07.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:07.989][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-06 01:09:07.994][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-06 01:09:07.996][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-06 01:09:07.999][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-06 01:09:08.001][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-06 01:09:08.003][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-06 01:09:08.005][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-06 01:09:08.007][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-06 01:09:08.009][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-06 01:09:08.012][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-06 01:09:08.014][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-06 01:09:08.016][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-06 01:09:08.018][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-06 01:09:08.020][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-06 01:09:08.022][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-06 01:09:08.024][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-06 01:09:08.025][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-06 01:09:08.027][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-06 01:09:08.029][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-06 01:09:08.031][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-06 01:09:08.033][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-06 01:09:08.035][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-06 01:09:08.036][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-06 01:09:08.038][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-06 01:09:08.041][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-06 01:09:08.043][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-06 01:09:08.045][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-06 01:09:08.047][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-06 01:09:08.049][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-06 01:09:08.051][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-06 01:09:08.052][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-06 01:09:08.054][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-06 01:09:08.056][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-06 01:09:08.057][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-06 01:09:08.061][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-06 01:09:08.062][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-06 01:09:08.064][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-06 01:09:08.066][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-06 01:09:08.067][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-06 01:09:08.069][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-06 01:09:08.071][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-06 01:09:08.072][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-06 01:09:08.074][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-06 01:09:08.076][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-06 01:09:08.077][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-06 01:09:08.079][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-06 01:09:08.081][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-06 01:09:08.082][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-06 01:09:08.084][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-06 01:09:08.086][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-06 01:09:08.087][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-06 01:09:08.089][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-06 01:09:08.090][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-06 01:09:08.092][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-06 01:09:08.094][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-06 01:09:08.095][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-06 01:09:08.097][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-06 01:09:08.098][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-06 01:09:08.100][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-06 01:09:08.102][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-06 01:09:08.104][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-06 01:09:08.105][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-06 01:09:08.107][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-06 01:09:08.109][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-06 01:09:08.110][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-06 01:09:08.112][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-06 01:09:08.113][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-06 01:09:08.115][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-06 01:09:08.117][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-06 01:09:08.118][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-06 01:09:08.120][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-06 01:09:08.122][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-06 01:09:08.123][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-06 01:09:08.125][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-06 01:09:08.126][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-06 01:09:08.128][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-06 01:09:08.130][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-06 01:09:08.132][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-06 01:09:08.134][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-06 01:09:08.135][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-06 01:09:08.137][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-06 01:09:08.139][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-06 01:09:08.140][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-06 01:09:08.176][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-06 01:09:08.180][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-06 01:09:08.184][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:09:08.186][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.188][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.298][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[2024-06-06 01:09:08.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:09:08.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:08.354][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-06 01:09:08.369][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:09:08.372][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:08.373][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-06 01:09:08.376][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:08.378][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:09:08.380][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:08.382][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:09:08.384][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:08.385][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:09:08.386][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:09:08.388][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:09:08.389][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:08.390][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-06 01:09:08.392][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-06 01:09:08.393][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-06 01:09:08.395][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-06 01:09:08.396][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:09:08.396][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:09:08.397][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:09:08.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:08.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:08.402][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:09:08.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:09:08.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:09:08.406][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:09:08.408][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-06 01:09:08.408][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-06 01:09:08.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:09:08.411][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:09:08.413][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-06 01:09:08.415][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:09:08.425][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-06 01:09:08.428][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-06 01:09:08.455][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:09:08.458][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-06 01:09:08.465][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:09:08.470][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-06 01:09:08.474][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-06 01:09:08.476][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-06 01:09:08.478][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-06 01:09:08.479][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-06 01:09:08.491][biodb::testThat]
biodb.INFO [2024-06-06 01:09:08.492][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-06 01:09:08.493][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:08.495][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:08.554][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-06-06 01:09:08.558][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-06 01:09:08.565][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-06 01:09:08.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:08.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:08.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:08.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:08.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:08.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:08.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:08.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:08.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:08.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:08.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-06 01:09:08.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-06 01:09:08.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.696][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-06 01:09:08.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-06 01:09:08.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.704][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-06 01:09:08.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-06 01:09:08.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.713][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:08.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:08.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.760][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:08.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:08.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.769][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:08.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:08.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.778][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:08.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:08.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.787][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-06 01:09:08.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:08.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.795][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-06 01:09:08.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:08.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.804][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:08.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:08.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.813][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:08.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:08.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:08.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:08.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.836][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-06 01:09:08.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.842][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-06 01:09:08.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:08.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:08.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.898][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-06 01:09:08.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:08.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.928][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:08.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:08.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:08.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:08.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:08.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:08.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.012][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.020][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.036][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:09.074][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-06 01:09:09.082][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-06 01:09:09.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-06 01:09:09.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.091][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-06 01:09:09.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-06 01:09:09.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.108][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-06 01:09:09.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-06 01:09:09.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.116][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-06 01:09:09.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-06 01:09:09.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.203][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.281][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.289][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.296][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:09.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.343][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.344][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.347][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.383][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.384][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.386][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.410][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.416][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.422][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.427][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.428][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.431][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.449][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:09.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:09.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:09.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:09.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:09.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.475][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:09.477][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:09.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.480][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:09.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:09.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.526][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.528][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.530][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.568][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.577][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.583][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.585][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.589][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.591][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.618][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.620][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.623][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.639][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.642][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.644][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.657][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:09.659][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:09.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.663][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.673][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.676][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.690][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.707][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.709][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.713][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.725][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.727][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.732][ef$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:09.756][biodb::testThat]
biodb.INFO [2024-06-06 01:09:09.758][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-06 01:09:09.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:09.761][biodb::testThat]
biodb.DEBUG[2024-06-06 01:09:09.776][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-06 01:09:09.785][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-06 01:09:09.795][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-06-06 01:09:09.798][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-06 01:09:09.803][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-06-06 01:09:09.805][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-06 01:09:09.842][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-06 01:09:09.845][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-06 01:09:09.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:09.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:09.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:09.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:09.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:09.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:09.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:09.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:09.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:09.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-06 01:09:09.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-06 01:09:09.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-06 01:09:09.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-06 01:09:09.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.909][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-06 01:09:09.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-06 01:09:09.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.915][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-06 01:09:09.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-06 01:09:09.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.922][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.930][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:09.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.936][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.943][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:09.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.960][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-06 01:09:09.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.967][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-06 01:09:09.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:09.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:09.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:09.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.983][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:09.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:09.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:09.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:09.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:09.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:09.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.002][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-06 01:09:10.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.008][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-06 01:09:10.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.014][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.025][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-06 01:09:10.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.030][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:10.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:10.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:10.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:10.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:10.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:10.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.075][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:10.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:10.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:10.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:10.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:10.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:10.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:10.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:10.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:10.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:10.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:10.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:10.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:10.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:10.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:10.133][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-06 01:09:10.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-06 01:09:10.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-06 01:09:10.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-06 01:09:10.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-06 01:09:10.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-06 01:09:10.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-06 01:09:10.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:10.187][biodb::testThat]
biodb.INFO [2024-06-06 01:09:10.189][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-06 01:09:10.190][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:10.191][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:10.201][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.203][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.208][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:10.210][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-06 01:09:10.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:10.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:10.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:10.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:10.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:10.291][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-06 01:09:10.298][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-06 01:09:10.321][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:10.323][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:10.325][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-06-06 01:09:11.334][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride does not exist.
biodb.TRACE[2024-06-06 01:09:11.335][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:11.338][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:11.341][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-06-06 01:09:11.948][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:09:11.953][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-06 01:09:11.981][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-06 01:09:11.987][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-06 01:09:12.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:12.034][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:12.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.037][ef$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:12.058][biodb::testThat]
biodb.INFO [2024-06-06 01:09:12.061][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-06 01:09:12.074][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:12.077][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:12.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:12.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:12.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:12.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:12.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:12.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:12.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:12.273][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-06 01:09:12.277][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-06 01:09:12.293][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-06 01:09:12.295][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-06 01:09:12.298][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-06 01:09:12.362][biodb::testThat]
biodb.INFO [2024-06-06 01:09:12.364][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-06 01:09:12.365][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:12.366][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:12.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-06 01:09:12.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-06 01:09:12.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-06 01:09:12.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-06 01:09:12.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-06 01:09:12.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-06 01:09:12.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.500][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-06 01:09:12.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-06 01:09:12.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.573][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-06 01:09:12.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-06 01:09:12.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-06 01:09:12.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-06 01:09:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.601][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-06 01:09:12.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-06 01:09:12.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:12.609][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-06 01:09:12.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-06 01:09:12.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:12.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:12.647][biodb::testThat]
biodb.INFO [2024-06-06 01:09:12.648][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-06 01:09:12.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:12.651][biodb::testThat]
biodb.INFO [2024-06-06 01:09:12.671][biodb::testThat]
biodb.INFO [2024-06-06 01:09:12.673][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-06 01:09:12.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:12.676][biodb::testThat]
biodb.INFO [2024-06-06 01:09:12.700][biodb::testThat]
biodb.INFO [2024-06-06 01:09:12.702][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-06 01:09:12.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:12.705][biodb::testThat]
biodb.DEBUG[2024-06-06 01:09:12.712][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-06 01:09:13.006][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-06 01:09:13.897][biodb::testThat]
biodb.INFO [2024-06-06 01:09:13.898][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-06 01:09:13.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:13.902][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:13.920][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:13.922][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:13.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:13.924][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:13.926][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:13.927][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:13.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:13.930][ef$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:13.932][biodb::testThat]
biodb.INFO [2024-06-06 01:09:13.935][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-06 01:09:13.936][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:13.937][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:13.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:13.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:13.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:13.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:13.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:13.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:13.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:13.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:13.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:13.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:13.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:14.082][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-06 01:09:14.087][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-06 01:09:14.090][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-06 01:09:14.093][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-06 01:09:14.095][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-06 01:09:14.171][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-06 01:09:14.175][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-06 01:09:14.176][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-06 01:09:14.178][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-06 01:09:14.181][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-06 01:09:14.229][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-06 01:09:14.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-06 01:09:14.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:14.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:14.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-06 01:09:14.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-06 01:09:14.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:14.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:14.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:14.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:14.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:14.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:14.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:14.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:14.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:14.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:14.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:14.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:14.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:14.318][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-06 01:09:14.342][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:14.344][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:14.362][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-06 01:09:14.662][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-06-06 01:09:14.663][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:14.666][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:14.668][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-06 01:09:20.259][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:09:20.264][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-06 01:09:20.441][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-06 01:09:22.497][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-06 01:09:22.501][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:22.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:22.505][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-06 01:09:24.045][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-06-06 01:09:24.047][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:24.049][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:24.051][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-06 01:09:24.738][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:09:24.741][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-06 01:09:24.746][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-06 01:09:24.792][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-06-06 01:09:24.796][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:24.797][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:24.800][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-06-06 01:09:25.088][doesRCurlRequestUrlExist] According to RCurl, URL 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 does not exist.
biodb.TRACE[2024-06-06 01:09:25.090][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:25.093][getUrlRequestResult] URL "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" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:25.095][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-06-06 01:09:25.695][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:09:25.698][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-06 01:09:25.703][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-06 01:09:25.841][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-06 01:09:25.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-06 01:09:25.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:25.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:25.862][biodb::testThat]
biodb.INFO [2024-06-06 01:09:25.864][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-06 01:09:25.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:25.866][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:25.870][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-06 01:09:25.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-06 01:09:25.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:25.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:25.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-06 01:09:25.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-06 01:09:25.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:25.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:25.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:25.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:25.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:25.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:25.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:25.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:25.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:25.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:25.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:25.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:25.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:25.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:25.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:25.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:25.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:25.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:25.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:25.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:25.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:25.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:25.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:25.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:25.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:25.931][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-06 01:09:25.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:25.937][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:25.939][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-06-06 01:09:26.248][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01 does not exist.
biodb.TRACE[2024-06-06 01:09:26.250][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:26.253][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:26.256][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-06-06 01:09:32.038][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:09:32.042][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-06 01:09:32.154][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-06 01:09:33.824][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-06 01:09:33.884][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-06 01:09:33.887][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-06 01:09:33.890][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-06-06 01:09:33.911][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-06-06 01:09:33.914][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-06 01:09:33.916][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-06 01:09:33.919][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-06 01:09:33.921][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-06 01:09:33.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:33.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:33.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:33.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:33.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:33.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:33.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:33.942][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-06 01:09:33.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:33.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:33.948][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-06 01:09:34.245][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:34.247][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:34.249][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:34.251][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-06 01:09:34.855][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:09:34.860][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-06 01:09:34.867][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-06 01:09:34.874][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-06 01:09:34.878][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-06 01:09:34.880][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-06 01:09:34.882][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-06 01:09:34.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:34.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:34.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:35.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:35.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:35.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:35.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:35.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-06 01:09:35.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-06 01:09:35.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-06 01:09:35.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-06 01:09:35.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.062][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-06 01:09:35.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-06 01:09:35.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.067][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-06 01:09:35.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-06 01:09:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.072][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:35.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:35.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.078][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:35.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:35.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.084][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:35.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:35.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.090][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:35.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:35.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.096][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-06 01:09:35.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:35.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.102][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-06 01:09:35.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:35.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.108][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:35.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:35.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.114][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:35.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:35.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:35.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:35.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.141][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-06 01:09:35.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.152][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-06 01:09:35.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:35.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:35.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.181][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-06 01:09:35.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.189][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.195][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.207][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:35.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:35.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:35.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:35.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:35.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:35.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:35.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:35.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-06 01:09:35.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-06 01:09:35.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.417][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-06 01:09:35.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-06 01:09:35.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.424][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-06 01:09:35.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-06 01:09:35.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.430][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:35.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:35.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.436][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:35.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-06 01:09:35.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:35.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:35.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:35.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-06 01:09:35.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.455][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-06 01:09:35.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:35.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.463][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-06 01:09:35.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:35.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:35.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:35.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-06 01:09:35.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-06 01:09:35.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:35.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:35.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.509][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-06 01:09:35.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.515][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-06 01:09:35.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:35.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:09:35.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.554][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-06 01:09:35.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:09:35.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.560][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.565][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.575][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:35.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:35.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:35.634][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-06 01:09:35.644][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-06 01:09:35.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:35.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:35.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:35.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:35.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:35.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:35.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:35.668][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.674][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.682][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.684][private$selectFields]
biodb.TRACE[2024-06-06 01:09:35.686][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:35.688][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:35.690][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.692][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.694][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.698][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.700][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.702][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.706][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.707][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.709][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.710][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.712][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.715][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.718][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:35.720][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.728][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.736][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.758][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-06 01:09:35.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:35.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:35.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:35.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:35.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:35.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:35.786][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.TRACE[2024-06-06 01:09:35.789][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.797][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.806][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.808][private$selectFields]
biodb.TRACE[2024-06-06 01:09:35.810][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:35.812][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:35.814][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.816][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.818][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.822][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.824][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.826][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.830][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.832][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.835][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.837][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.839][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.843][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.845][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:35.847][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.856][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.864][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.873][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-06 01:09:35.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:35.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:35.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:35.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:35.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:35.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:35.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:35.904][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.912][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.920][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.921][private$selectFields]
biodb.TRACE[2024-06-06 01:09:35.922][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:35.923][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:35.924][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.926][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.928][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.932][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.934][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.936][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.938][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.939][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.941][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:35.942][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.944][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.947][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:35.949][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.958][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.966][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:35.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:35.973][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-06 01:09:35.975][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-06 01:09:35.976][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-06 01:09:35.993][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-06 01:09:35.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-06 01:09:35.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:35.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:36.006][biodb::testThat]
biodb.INFO [2024-06-06 01:09:36.007][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-06 01:09:36.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:36.010][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:36.015][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-06 01:09:36.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-06 01:09:36.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:36.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:36.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-06 01:09:36.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-06 01:09:36.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:36.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:36.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:36.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:36.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:36.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:36.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:36.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:36.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:36.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:36.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:36.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:36.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:36.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:36.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:36.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:36.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:36.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:36.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:36.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:36.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:36.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:36.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:36.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:36.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:36.159][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-06-06 01:09:36.165][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:36.167][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:36.171][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-06-06 01:09:36.479][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375 does not exist.
biodb.TRACE[2024-06-06 01:09:36.481][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:36.483][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:36.485][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-06-06 01:09:42.034][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:09:42.038][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-06 01:09:42.400][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-06 01:09:44.155][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-06 01:09:44.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:44.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:44.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:44.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:44.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:44.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:44.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:44.219][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.225][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.247][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.249][private$selectFields]
biodb.TRACE[2024-06-06 01:09:44.250][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:44.251][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:44.253][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.254][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.255][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.258][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.259][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.260][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.262][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.264][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.273][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.275][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.276][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.279][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.280][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:44.281][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.286][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.291][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.297][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-06 01:09:44.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:44.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:44.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:44.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:44.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:44.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:44.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:44.324][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.329][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.334][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.336][private$selectFields]
biodb.TRACE[2024-06-06 01:09:44.337][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:44.338][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:44.339][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.340][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.342][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.344][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.345][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.347][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.349][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.350][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.352][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.353][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.354][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.358][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:44.359][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.364][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.369][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.374][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-06 01:09:44.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:44.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:44.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:44.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:44.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:44.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:44.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:44.401][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.409][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.415][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.416][private$selectFields]
biodb.TRACE[2024-06-06 01:09:44.417][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:44.418][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:44.420][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.422][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.424][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.428][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.429][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.432][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.436][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.437][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.439][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:44.440][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.441][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.444][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.445][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:44.446][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.451][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.456][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:44.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.462][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-06 01:09:44.463][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-06 01:09:44.464][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-06 01:09:44.493][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-06 01:09:44.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-06 01:09:44.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:44.516][biodb::testThat]
biodb.INFO [2024-06-06 01:09:44.518][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-06 01:09:44.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:44.520][biodb::testThat]
biodb.TRACE[2024-06-06 01:09:44.525][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-06 01:09:44.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-06 01:09:44.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-06 01:09:44.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-06 01:09:44.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:44.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:44.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:44.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:44.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:44.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:44.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:44.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:44.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:09:44.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:44.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:44.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:44.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:44.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:44.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:44.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:44.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:44.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:44.582][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-06 01:09:44.587][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-06 01:09:44.589][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-06 01:09:44.591][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-06 01:09:44.767][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-06 01:09:46.463][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-06 01:09:46.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:46.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:46.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:46.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:46.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:46.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:46.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:46.480][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.485][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.490][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.492][private$selectFields]
biodb.TRACE[2024-06-06 01:09:46.493][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:46.494][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:46.495][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.496][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.498][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.500][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.501][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.503][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.505][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.506][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.507][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.509][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.510][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.512][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.514][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:46.515][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.520][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.526][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.532][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-06 01:09:46.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:46.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:46.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:46.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:46.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:46.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:46.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:46.548][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.553][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.558][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.559][private$selectFields]
biodb.TRACE[2024-06-06 01:09:46.560][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:46.561][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:46.563][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.564][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.565][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.568][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.569][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.570][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.573][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.574][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.575][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.576][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.578][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.580][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.581][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:46.582][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.587][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.592][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.598][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-06 01:09:46.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:46.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:46.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:46.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:46.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:46.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:46.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:46.623][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.633][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.634][private$selectFields]
biodb.TRACE[2024-06-06 01:09:46.635][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-06 01:09:46.636][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-06 01:09:46.638][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.639][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.640][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.643][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.644][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.645][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.648][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.649][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.650][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-06 01:09:46.652][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.654][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.657][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.659][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-06 01:09:46.661][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.669][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.675][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:46.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:46.681][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-06 01:09:46.682][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-06 01:09:46.684][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-06 01:09:46.856][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-06 01:09:46.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-06 01:09:46.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:46.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-06 01:09:46.867][biodb::testThat]
biodb.INFO [2024-06-06 01:09:46.869][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-06 01:09:46.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:46.871][biodb::testThat]
biodb.DEBUG[2024-06-06 01:09:46.874][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-06 01:09:46.875][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-06 01:09:46.877][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-06 01:09:46.879][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-06 01:09:46.881][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-06 01:09:46.882][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-06 01:09:46.884][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-06 01:09:46.885][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-06 01:09:46.886][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-06 01:09:46.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:46.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:46.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:46.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:46.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:46.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:46.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:46.928][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-06 01:09:46.931][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:46.933][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:46.934][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:47.227][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:47.229][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:47.230][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:47.232][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:47.842][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:47.845][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:47.847][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:47.849][rule$waitAsNeeded] Wait 0.0853939 second(s).
biodb.TRACE[2024-06-06 01:09:47.951][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:48.255][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:48.257][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:48.258][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:48.260][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:48.860][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:48.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:48.863][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:48.864][rule$waitAsNeeded] Wait 0.085366 second(s).
biodb.TRACE[2024-06-06 01:09:48.953][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:49.264][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:49.265][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:49.267][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:49.268][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:49.863][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:49.865][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:49.867][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:49.870][rule$waitAsNeeded] Wait 0.0828221 second(s).
biodb.TRACE[2024-06-06 01:09:49.971][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:50.266][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:50.268][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:50.269][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:50.271][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:50.865][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:50.867][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:50.870][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:50.872][rule$waitAsNeeded] Wait 0.098736 second(s).
biodb.TRACE[2024-06-06 01:09:50.989][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:51.302][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:51.304][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:51.305][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:51.307][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:51.914][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:51.916][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:51.918][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:51.920][rule$waitAsNeeded] Wait 0.0684161 second(s).
biodb.TRACE[2024-06-06 01:09:51.991][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:52.332][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:52.334][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:52.335][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:52.337][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:52.932][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:52.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:52.935][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:52.937][rule$waitAsNeeded] Wait 0.0536699 second(s).
biodb.TRACE[2024-06-06 01:09:52.994][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:53.291][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:53.292][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:53.294][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:53.295][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:53.887][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:53.889][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:53.890][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:53.892][rule$waitAsNeeded] Wait 0.101242 second(s).
biodb.TRACE[2024-06-06 01:09:53.997][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:54.301][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:54.321][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:54.324][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:54.326][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:54.922][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:54.923][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:54.925][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:54.927][rule$waitAsNeeded] Wait 0.0698111 second(s).
biodb.TRACE[2024-06-06 01:09:55.015][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:55.315][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:55.317][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:55.318][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:55.319][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:55.923][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:55.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:55.926][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:55.927][rule$waitAsNeeded] Wait 0.0865669 second(s).
biodb.TRACE[2024-06-06 01:09:56.017][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-06 01:09:56.330][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:56.331][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:56.334][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:56.335][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-06 01:09:56.942][private$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.INFO [2024-06-06 01:09:56.945][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-06-06 01:09:56.948][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-06 01:09:56.950][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-06 01:09:56.952][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-06 01:09:56.954][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-06 01:09:56.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:56.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:56.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:56.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:56.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:56.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:56.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:09:56.991][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:56.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:56.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:56.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:56.997][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:56.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:09:56.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:57.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:57.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:57.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:57.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:57.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:57.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:57.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:57.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:57.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:57.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:57.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:57.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:57.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:57.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:57.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:57.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:57.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:57.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:09:57.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:09:57.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:09:57.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:09:57.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:09:57.034][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-06 01:09:57.035][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-06 01:09:57.049][biodb::testThat]
biodb.INFO [2024-06-06 01:09:57.050][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-06 01:09:57.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:09:57.053][biodb::testThat]
biodb.DEBUG[2024-06-06 01:09:57.094][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-06 01:09:57.096][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-06 01:09:57.098][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-06 01:09:57.100][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-06 01:09:57.102][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-06 01:09:57.103][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-06 01:09:57.105][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-06 01:09:57.106][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-06 01:09:57.107][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-06 01:09:57.109][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-06 01:09:57.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:09:57.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:09:57.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:09:57.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:09:57.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:09:57.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:09:57.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:09:57.130][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-06 01:09:57.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:57.137][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:09:57.139][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:09:57.435][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:57.436][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:57.437][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:57.439][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:09:58.038][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:58.040][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:58.042][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:58.043][rule$waitAsNeeded] Wait 0.095974 second(s).
biodb.TRACE[2024-06-06 01:09:58.147][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:09:58.448][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:58.450][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:58.451][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:58.453][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:09:59.040][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:09:59.043][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:09:59.045][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:09:59.047][rule$waitAsNeeded] Wait 0.099026 second(s).
biodb.TRACE[2024-06-06 01:09:59.164][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:09:59.478][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:09:59.480][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:09:59.481][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:09:59.483][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:10:00.089][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:00.092][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:00.094][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:00.096][rule$waitAsNeeded] Wait 0.0670712 second(s).
biodb.TRACE[2024-06-06 01:10:00.181][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:10:00.477][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:00.479][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:00.480][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:00.482][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:10:01.091][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:01.093][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:01.095][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:01.098][rule$waitAsNeeded] Wait 0.0832119 second(s).
biodb.TRACE[2024-06-06 01:10:01.199][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:10:01.515][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:01.517][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:01.520][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:01.522][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:10:02.124][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:02.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:02.129][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:02.131][rule$waitAsNeeded] Wait 0.0678351 second(s).
biodb.TRACE[2024-06-06 01:10:02.217][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:10:02.524][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:02.526][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:02.528][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:02.529][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:10:03.126][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:03.128][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:03.130][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:03.132][rule$waitAsNeeded] Wait 0.0837188 second(s).
biodb.TRACE[2024-06-06 01:10:03.235][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:10:03.544][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:03.545][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:03.547][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:03.548][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:10:04.143][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:04.146][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:04.148][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:04.150][rule$waitAsNeeded] Wait 0.08446 second(s).
biodb.TRACE[2024-06-06 01:10:04.236][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:10:04.538][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:04.540][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:04.542][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:04.543][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:10:05.145][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:05.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:05.149][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:05.151][rule$waitAsNeeded] Wait 0.0847111 second(s).
biodb.TRACE[2024-06-06 01:10:05.253][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:10:05.556][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:05.558][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:05.560][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:05.561][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:10:06.163][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:06.165][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:06.167][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:06.168][rule$waitAsNeeded] Wait 0.0841689 second(s).
biodb.TRACE[2024-06-06 01:10:06.256][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-06 01:10:06.593][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:06.595][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:06.597][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:06.599][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-06 01:10:07.195][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:07.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:07.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:07.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:07.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:07.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:07.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:07.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:07.217][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-06 01:10:07.221][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:07.223][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:07.224][rule$waitAsNeeded] Wait 0.030457 second(s).
biodb.TRACE[2024-06-06 01:10:07.257][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:07.563][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:07.565][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:07.566][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:07.568][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:08.183][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:08.186][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:08.188][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:08.190][rule$waitAsNeeded] Wait 0.0671391 second(s).
biodb.TRACE[2024-06-06 01:10:08.260][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:08.568][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:08.570][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:08.571][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:08.573][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:09.173][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:09.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:09.177][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:09.180][rule$waitAsNeeded] Wait 0.0808079 second(s).
biodb.TRACE[2024-06-06 01:10:09.266][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:09.568][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:09.570][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:09.572][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:09.575][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:10.163][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:10.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:10.168][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:10.170][rule$waitAsNeeded] Wait 0.095355 second(s).
biodb.TRACE[2024-06-06 01:10:10.272][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:10.561][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:10.562][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:10.564][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:10.565][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:11.181][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:11.184][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:11.186][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:11.188][rule$waitAsNeeded] Wait 0.0831289 second(s).
biodb.TRACE[2024-06-06 01:10:11.278][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:11.595][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:11.598][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:11.600][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:11.602][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:12.205][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:12.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:12.209][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:12.212][rule$waitAsNeeded] Wait 0.0654461 second(s).
biodb.TRACE[2024-06-06 01:10:12.283][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:12.580][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:12.582][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:12.584][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:12.585][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:13.176][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:13.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:13.179][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:13.181][rule$waitAsNeeded] Wait 0.101135 second(s).
biodb.TRACE[2024-06-06 01:10:13.285][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:13.588][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:13.590][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:13.591][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:13.593][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:14.178][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:14.180][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:14.181][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:14.183][rule$waitAsNeeded] Wait 0.101669 second(s).
biodb.TRACE[2024-06-06 01:10:14.287][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:14.601][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:14.602][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:14.604][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:14.605][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:15.197][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:15.199][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:15.202][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:15.204][rule$waitAsNeeded] Wait 0.0834789 second(s).
biodb.TRACE[2024-06-06 01:10:15.326][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:15.636][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:15.637][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:15.639][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:15.640][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:16.233][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:16.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:16.237][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:16.239][rule$waitAsNeeded] Wait 0.081563 second(s).
biodb.TRACE[2024-06-06 01:10:16.340][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-06 01:10:16.653][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:16.655][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:16.657][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:16.659][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-06 01:10:17.250][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-06 01:10:17.255][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-06-06 01:10:17.258][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-06 01:10:17.260][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-06 01:10:17.262][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-06 01:10:17.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:17.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:17.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:17.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:17.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:17.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:17.278][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[2024-06-06 01:10:17.280][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:17.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:17.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.287][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:17.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:17.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:10:17.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:17.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:17.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:17.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:17.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:17.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:17.311][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.TRACE[2024-06-06 01:10:17.314][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:17.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:17.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:17.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:17.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:17.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:17.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:17.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:17.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:10:17.388][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-06 01:10:17.390][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-06 01:10:17.391][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-06 01:10:17.775][biodb::testThat]
biodb.INFO [2024-06-06 01:10:17.777][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-06 01:10:17.779][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:10:17.782][biodb::testThat]
biodb.INFO [2024-06-06 01:10:17.852][biodb::testThat]
biodb.INFO [2024-06-06 01:10:17.854][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-06 01:10:17.856][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:10:17.857][biodb::testThat]
biodb.INFO [2024-06-06 01:10:17.876][biodb::testThat]
biodb.INFO [2024-06-06 01:10:17.878][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-06 01:10:17.879][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:10:17.880][biodb::testThat]
biodb.DEBUG[2024-06-06 01:10:17.884][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-06 01:10:17.888][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:17.889][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:10:17.891][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-06 01:10:18.194][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV does not exist.
biodb.TRACE[2024-06-06 01:10:18.196][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:18.198][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:18.201][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-06 01:10:24.058][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:10:24.062][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-06 01:10:24.403][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-06 01:10:25.961][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-06 01:10:25.962][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-06 01:10:25.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:25.965][ef$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:25.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:10:25.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-06 01:10:25.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:25.971][ef$get] fields variable is a list.
biodb.INFO [2024-06-06 01:10:25.974][biodb::testThat]
biodb.INFO [2024-06-06 01:10:25.976][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-06 01:10:25.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:10:25.978][biodb::testThat]
biodb.ERROR[2024-06-06 01:10:26.005][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-06 01:10:26.026][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-06 01:10:26.050][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-06 01:10:26.052][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-06 01:10:26.054][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-06 01:10:26.055][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-06 01:10:26.056][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.058][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.061][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-06 01:10:26.097][biodb::testContext]
biodb.INFO [2024-06-06 01:10:26.099][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-06 01:10:26.101][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-06 01:10:26.103][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-06 01:10:26.105][biodb::testContext]
biodb.INFO [2024-06-06 01:10:26.110][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-06 01:10:26.113][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-06 01:10:26.119][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:10:26.121][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-06 01:10:26.122][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-06 01:10:26.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.126][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[2024-06-06 01:10:26.127][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-06 01:10:26.128][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-06 01:10:26.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.139][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-06 01:10:26.140][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-06 01:10:26.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.145][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-06 01:10:26.147][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-06 01:10:26.148][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-06 01:10:26.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.155][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-06 01:10:26.157][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-06 01:10:26.158][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-06 01:10:26.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.163][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-06 01:10:26.164][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-06 01:10:26.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.169][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-06 01:10:26.170][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-06 01:10:26.171][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-06 01:10:26.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.176][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-06 01:10:26.177][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-06 01:10:26.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.182][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-06 01:10:26.183][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-06 01:10:26.185][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-06 01:10:26.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.190][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-06 01:10:26.191][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-06 01:10:26.192][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-06 01:10:26.194][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-06 01:10:26.195][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-06 01:10:26.196][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-06 01:10:26.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.201][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-06 01:10:26.202][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-06 01:10:26.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.209][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-06 01:10:26.210][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-06 01:10:26.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.216][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-06 01:10:26.217][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-06 01:10:26.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.222][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-06 01:10:26.224][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-06 01:10:26.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.229][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-06 01:10:26.230][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-06 01:10:26.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.235][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-06 01:10:26.238][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-06 01:10:26.242][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-06 01:10:26.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.254][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-06 01:10:26.255][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-06 01:10:26.257][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-06 01:10:26.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.262][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-06 01:10:26.264][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.265][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-06 01:10:26.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:26.269][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.271][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.272][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.273][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.274][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:10:26.276][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:26.277][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.278][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-06 01:10:26.280][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:26.281][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.282][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.283][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:10:26.283][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:10:26.283][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-06 01:10:26.283][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-06 01:10:26.283][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-06 01:10:26.285][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:26.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.288][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:26.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.292][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.293][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:26.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:26.297][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.298][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.299][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-06 01:10:26.301][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.303][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-06 01:10:26.304][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.305][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:26.307][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.308][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.309][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.310][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.312][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-06 01:10:26.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:26.314][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.315][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-06 01:10:26.316][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:26.318][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.319][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.320][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:10:26.320][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:10:26.320][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-06 01:10:26.320][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-06 01:10:26.320][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-06 01:10:26.322][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:26.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.325][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:26.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.329][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.330][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.331][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:26.332][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:26.334][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.335][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.337][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-06 01:10:26.340][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.342][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-06 01:10:26.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.346][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:26.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.351][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.352][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.354][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.355][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:10:26.356][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:26.358][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.359][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-06 01:10:26.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:26.361][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.363][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.364][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.365][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:26.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.369][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:26.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.372][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.374][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.375][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:26.376][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:26.377][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.392][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.394][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-06 01:10:26.396][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.397][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-06 01:10:26.399][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.400][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:26.401][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.402][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.404][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.406][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-06 01:10:26.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:26.409][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.410][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-06 01:10:26.411][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:26.412][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.414][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.415][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.416][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:26.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.420][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:26.421][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.423][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.424][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.426][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:26.427][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:26.428][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.429][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.431][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:10:26.432][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.532][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-06 01:10:26.534][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-06 01:10:26.536][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-06 01:10:26.537][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-06 01:10:26.539][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-06 01:10:26.542][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-06 01:10:26.543][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-06 01:10:26.545][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-06 01:10:26.547][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-06 01:10:26.549][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-06 01:10:26.550][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-06 01:10:26.552][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-06 01:10:26.554][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-06 01:10:26.555][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-06 01:10:26.557][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-06 01:10:26.559][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-06 01:10:26.560][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-06 01:10:26.562][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-06 01:10:26.564][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-06 01:10:26.565][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-06 01:10:26.567][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-06 01:10:26.569][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-06 01:10:26.571][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-06 01:10:26.572][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-06 01:10:26.574][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-06 01:10:26.576][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-06 01:10:26.578][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-06 01:10:26.579][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-06 01:10:26.581][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-06 01:10:26.583][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-06 01:10:26.584][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-06 01:10:26.586][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-06 01:10:26.588][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-06 01:10:26.589][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-06 01:10:26.591][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-06 01:10:26.593][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-06 01:10:26.594][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-06 01:10:26.596][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-06 01:10:26.598][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-06 01:10:26.599][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-06 01:10:26.601][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-06 01:10:26.603][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-06 01:10:26.604][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-06 01:10:26.606][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-06 01:10:26.608][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-06 01:10:26.610][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-06 01:10:26.611][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-06 01:10:26.613][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-06 01:10:26.614][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-06 01:10:26.616][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-06 01:10:26.618][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-06 01:10:26.619][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-06 01:10:26.621][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-06 01:10:26.623][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-06 01:10:26.625][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-06 01:10:26.626][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-06 01:10:26.628][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-06 01:10:26.630][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-06 01:10:26.631][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-06 01:10:26.633][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-06 01:10:26.635][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-06 01:10:26.636][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-06 01:10:26.638][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-06 01:10:26.640][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-06 01:10:26.641][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-06 01:10:26.643][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-06 01:10:26.645][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-06 01:10:26.646][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-06 01:10:26.648][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-06 01:10:26.649][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-06 01:10:26.651][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-06 01:10:26.653][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-06 01:10:26.654][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-06 01:10:26.656][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-06 01:10:26.658][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-06 01:10:26.660][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-06 01:10:26.661][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-06 01:10:26.663][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-06 01:10:26.665][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-06 01:10:26.666][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-06 01:10:26.668][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-06 01:10:26.670][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-06 01:10:26.671][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-06 01:10:26.673][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-06 01:10:26.676][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-06 01:10:26.677][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:10:26.678][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.681][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.809][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[2024-06-06 01:10:26.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:26.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:26.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:26.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:26.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:26.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:26.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:26.833][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[2024-06-06 01:10:26.836][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-06 01:10:26.839][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:10:26.841][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.843][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.844][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:26.847][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.848][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.849][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.850][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.851][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:10:26.853][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:26.854][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.855][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-06 01:10:26.856][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-06 01:10:26.858][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-06 01:10:26.859][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:26.860][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:10:26.860][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:10:26.861][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:26.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:26.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:26.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:26.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:26.870][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-06 01:10:26.870][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-06 01:10:26.871][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:26.872][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:26.874][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:26.875][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:26.876][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-06 01:10:26.878][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-06 01:10:26.882][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:10:26.883][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-06 01:10:26.885][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:10:26.888][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-06 01:10:26.890][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-06 01:10:26.892][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-06 01:10:26.895][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-06 01:10:26.897][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-06 01:10:26.900][biodb::testThat]
biodb.INFO [2024-06-06 01:10:26.901][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-06 01:10:26.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:10:26.905][biodb::testThat]
biodb.DEBUG[2024-06-06 01:10:26.911][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-06-06 01:10:26.919][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:26.921][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:10:26.923][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-06 01:10:27.216][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride does not exist.
biodb.TRACE[2024-06-06 01:10:27.217][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:27.219][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:27.221][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-06-06 01:10:27.817][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:10:27.820][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-06 01:10:27.826][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-06 01:10:27.840][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-06-06 01:10:27.844][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:27.846][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:27.847][rule$waitAsNeeded] Wait 0.075213 second(s).
biodb.TRACE[2024-06-06 01:10:27.927][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-06 01:10:28.219][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty does not exist.
biodb.TRACE[2024-06-06 01:10:28.220][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:28.222][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:28.224][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-06-06 01:10:28.817][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:10:28.820][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-06 01:10:28.825][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-06 01:10:28.853][biodb::testThat]
biodb.INFO [2024-06-06 01:10:28.855][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-06 01:10:28.857][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:10:28.858][biodb::testThat]
biodb.INFO [2024-06-06 01:10:28.898][biodb::testThat]
biodb.INFO [2024-06-06 01:10:28.900][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-06 01:10:28.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:10:28.904][biodb::testThat]
biodb.DEBUG[2024-06-06 01:10:28.910][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-06 01:10:28.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:28.919][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:28.920][rule$waitAsNeeded] Wait 0.00485992 second(s).
biodb.TRACE[2024-06-06 01:10:28.933][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-06 01:10:29.225][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-06-06 01:10:29.227][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:29.229][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:29.230][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-06 01:10:29.642][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:10:29.645][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-06 01:10:29.653][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-06 01:10:29.661][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-06 01:10:29.665][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-06 01:10:29.666][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-06 01:10:29.668][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-06 01:10:29.676][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-06 01:10:29.686][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-06-06 01:10:29.690][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:29.691][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:29.693][rule$waitAsNeeded] Wait 0.239616 second(s).
biodb.TRACE[2024-06-06 01:10:29.938][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-06 01:10:30.235][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-06-06 01:10:30.237][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:30.239][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:30.241][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-06-06 01:10:30.652][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:10:30.669][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-06 01:10:30.675][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-06 01:10:30.684][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-06-06 01:10:30.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:30.690][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:30.691][rule$waitAsNeeded] Wait 0.246433 second(s).
biodb.TRACE[2024-06-06 01:10:30.943][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-06 01:10:31.234][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid does not exist.
biodb.TRACE[2024-06-06 01:10:31.235][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:31.237][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:31.239][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-06 01:10:32.735][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:10:32.740][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-06 01:10:32.766][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-06 01:10:33.061][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-06-06 01:10:33.068][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:33.071][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:10:33.074][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-06 01:10:33.372][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6 does not exist.
biodb.TRACE[2024-06-06 01:10:33.374][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:33.376][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:33.378][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-06 01:10:34.948][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-06 01:10:34.951][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-06 01:10:34.970][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-06 01:10:35.249][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-06 01:10:35.251][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-06 01:10:35.252][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-06 01:10:35.254][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-06 01:10:35.255][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:35.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:35.257][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.260][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-06 01:10:35.278][biodb::testContext]
biodb.INFO [2024-06-06 01:10:35.279][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-06 01:10:35.281][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-06 01:10:35.282][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-06 01:10:35.283][biodb::testContext]
biodb.INFO [2024-06-06 01:10:35.286][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-06 01:10:35.289][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-06 01:10:35.295][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:10:35.297][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-06 01:10:35.298][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-06 01:10:35.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.303][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-06 01:10:35.304][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-06 01:10:35.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.309][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-06 01:10:35.311][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-06 01:10:35.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.316][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-06 01:10:35.318][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-06 01:10:35.319][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-06 01:10:35.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.324][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-06 01:10:35.325][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-06 01:10:35.326][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-06 01:10:35.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.330][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[2024-06-06 01:10:35.332][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-06 01:10:35.333][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-06 01:10:35.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.338][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-06 01:10:35.339][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-06 01:10:35.340][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-06 01:10:35.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.345][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-06 01:10:35.346][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-06 01:10:35.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.351][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-06 01:10:35.352][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-06 01:10:35.354][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-06 01:10:35.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.359][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-06 01:10:35.360][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-06 01:10:35.361][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-06 01:10:35.363][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-06 01:10:35.364][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-06 01:10:35.365][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-06 01:10:35.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.370][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-06 01:10:35.372][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-06 01:10:35.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.378][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-06 01:10:35.379][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-06 01:10:35.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.384][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-06 01:10:35.386][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-06 01:10:35.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.391][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-06 01:10:35.392][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-06 01:10:35.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.397][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-06 01:10:35.399][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-06 01:10:35.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.403][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-06 01:10:35.405][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-06 01:10:35.409][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-06 01:10:35.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.414][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-06 01:10:35.415][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-06 01:10:35.417][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-06 01:10:35.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.420][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[2024-06-06 01:10:35.422][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-06 01:10:35.425][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.427][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-06 01:10:35.429][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.431][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:35.433][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.435][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.437][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.439][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.441][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:10:35.443][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:35.446][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.448][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-06 01:10:35.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:35.452][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.454][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.456][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:10:35.456][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:10:35.456][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-06 01:10:35.456][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-06 01:10:35.456][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-06 01:10:35.458][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:35.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:35.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:35.465][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:35.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:35.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:35.471][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.473][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:35.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:35.479][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.481][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.483][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-06 01:10:35.487][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.489][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-06 01:10:35.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.493][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:35.495][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.500][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.504][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-06 01:10:35.506][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:35.508][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.510][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-06 01:10:35.512][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:35.514][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.518][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:10:35.518][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:10:35.518][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-06 01:10:35.518][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-06 01:10:35.518][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-06 01:10:35.520][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:35.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:35.524][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:35.526][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:35.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:35.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:35.532][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.534][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.536][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:35.538][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:35.540][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.542][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.544][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-06 01:10:35.547][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.550][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-06 01:10:35.552][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.554][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:35.556][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.560][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.563][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.565][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:10:35.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:35.568][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.569][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-06 01:10:35.570][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:35.572][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.573][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.575][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.576][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:35.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:35.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:35.580][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:35.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:35.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:35.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.585][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.586][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:35.587][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:35.588][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.589][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.591][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-06 01:10:35.593][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.594][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-06 01:10:35.616][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.619][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:35.621][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.624][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.626][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.628][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.630][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-06 01:10:35.632][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:35.634][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.636][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-06 01:10:35.638][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:35.640][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.642][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:35.644][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.647][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:35.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:35.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:35.652][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:35.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:35.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:35.658][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:35.660][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.662][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:35.663][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:35.665][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:35.666][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:35.669][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:10:35.670][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.786][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[2024-06-06 01:10:35.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.797][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[2024-06-06 01:10:35.799][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-06 01:10:35.800][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-06 01:10:35.802][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-06 01:10:35.804][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-06 01:10:35.805][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-06 01:10:35.807][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-06 01:10:35.809][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-06 01:10:35.810][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-06 01:10:35.812][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-06 01:10:35.814][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-06 01:10:35.815][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-06 01:10:35.817][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-06 01:10:35.818][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-06 01:10:35.820][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-06 01:10:35.822][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-06 01:10:35.823][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-06 01:10:35.825][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-06 01:10:35.827][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-06 01:10:35.828][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-06 01:10:35.831][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-06 01:10:35.833][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-06 01:10:35.835][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-06 01:10:35.837][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-06 01:10:35.839][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-06 01:10:35.840][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-06 01:10:35.842][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-06 01:10:35.845][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-06 01:10:35.847][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-06 01:10:35.850][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-06 01:10:35.853][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-06 01:10:35.856][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-06 01:10:35.858][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-06 01:10:35.860][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-06 01:10:35.862][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-06 01:10:35.864][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-06 01:10:35.865][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-06 01:10:35.867][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-06 01:10:35.869][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-06 01:10:35.870][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-06 01:10:35.872][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-06 01:10:35.874][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-06 01:10:35.876][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-06 01:10:35.877][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-06 01:10:35.879][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-06 01:10:35.880][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-06 01:10:35.882][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-06 01:10:35.885][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-06 01:10:35.888][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-06 01:10:35.890][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-06 01:10:35.893][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-06 01:10:35.896][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-06 01:10:35.898][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-06 01:10:35.901][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-06 01:10:35.902][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-06 01:10:35.904][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-06 01:10:35.905][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-06 01:10:35.907][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-06 01:10:35.909][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-06 01:10:35.910][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-06 01:10:35.912][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-06 01:10:35.914][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-06 01:10:35.916][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-06 01:10:35.918][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-06 01:10:35.921][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-06 01:10:35.924][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-06 01:10:35.926][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-06 01:10:35.928][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-06 01:10:35.929][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-06 01:10:35.931][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-06 01:10:35.932][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-06 01:10:35.934][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-06 01:10:35.936][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-06 01:10:35.937][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-06 01:10:35.939][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-06 01:10:35.940][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-06 01:10:35.942][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-06 01:10:35.944][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-06 01:10:35.945][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-06 01:10:35.947][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-06 01:10:35.948][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-06 01:10:35.950][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-06 01:10:35.952][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-06 01:10:35.953][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-06 01:10:35.955][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-06 01:10:35.958][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-06 01:10:35.959][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-06 01:10:35.960][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.962][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:35.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:35.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:35.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:35.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:35.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:35.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:35.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:35.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:35.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:35.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:35.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:35.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:35.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:35.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.040][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[2024-06-06 01:10:36.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.071][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[2024-06-06 01:10:36.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.101][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[2024-06-06 01:10:36.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.109][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[2024-06-06 01:10:36.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-06 01:10:36.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:36.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:36.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:36.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:36.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:36.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:36.121][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-06 01:10:36.124][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:10:36.126][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:36.127][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-06 01:10:36.128][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:36.129][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-06 01:10:36.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:36.132][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-06 01:10:36.133][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:36.134][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-06 01:10:36.135][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-06 01:10:36.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-06 01:10:36.138][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:36.139][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-06 01:10:36.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-06 01:10:36.141][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-06 01:10:36.143][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-06 01:10:36.144][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-06 01:10:36.144][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-06 01:10:36.145][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-06 01:10:36.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:36.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:36.148][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-06 01:10:36.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-06 01:10:36.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-06 01:10:36.152][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-06 01:10:36.153][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-06 01:10:36.153][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-06 01:10:36.154][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-06 01:10:36.155][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-06 01:10:36.156][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-06 01:10:36.158][self$setPropertyValue]
biodb.DEBUG[2024-06-06 01:10:36.159][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-06 01:10:36.161][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-06 01:10:36.164][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:10:36.165][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-06 01:10:36.167][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-06 01:10:36.169][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-06 01:10:36.170][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-06 01:10:36.171][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-06 01:10:36.173][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-06 01:10:36.174][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-06 01:10:36.176][biodb::testThat]
biodb.INFO [2024-06-06 01:10:36.177][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-06-06 01:10:36.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-06 01:10:36.180][biodb::testThat]
biodb.DEBUG[2024-06-06 01:10:36.184][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-06 01:10:36.189][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-06 01:10:36.191][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-06 01:10:36.192][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-06 01:10:36.360][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-06 01:10:38.099][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-06 01:10:38.101][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-06 01:10:38.103][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-06 01:10:38.105][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-06 01:10:38.107][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-06 01:10:38.108][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-06 01:10:38.109][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-06 01:10:38.111][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-06 01:10:38.112][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-06 01:10:38.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:38.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:38.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:38.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:38.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:38.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:38.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:38.977][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-06-06 01:10:38.980][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:38.982][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:10:38.983][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:39.273][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:39.274][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:39.275][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:39.277][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:39.859][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:39.860][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:39.862][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:39.863][rule$waitAsNeeded] Wait 0.119861 second(s).
biodb.TRACE[2024-06-06 01:10:39.999][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:40.298][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:40.299][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:40.301][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:40.302][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:40.892][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:40.894][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:40.895][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:40.897][rule$waitAsNeeded] Wait 0.100995 second(s).
biodb.TRACE[2024-06-06 01:10:41.001][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:41.291][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:41.293][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:41.294][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:41.295][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:41.880][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:41.883][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:41.885][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:41.888][rule$waitAsNeeded] Wait 0.11304 second(s).
biodb.TRACE[2024-06-06 01:10:42.003][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:42.298][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:42.299][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:42.301][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:42.302][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:42.897][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:42.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:42.900][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:42.901][rule$waitAsNeeded] Wait 0.101138 second(s).
biodb.TRACE[2024-06-06 01:10:43.005][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:43.296][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:43.297][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:43.299][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:43.300][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:43.900][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:43.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:43.902][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:43.904][rule$waitAsNeeded] Wait 0.101235 second(s).
biodb.TRACE[2024-06-06 01:10:44.008][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:44.302][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:44.303][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:44.304][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:44.306][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:44.902][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:44.904][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:44.905][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:44.907][rule$waitAsNeeded] Wait 0.100267 second(s).
biodb.TRACE[2024-06-06 01:10:45.010][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:45.308][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:45.309][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:45.310][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:45.312][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:45.905][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:45.906][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:45.908][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:45.909][rule$waitAsNeeded] Wait 0.100853 second(s).
biodb.TRACE[2024-06-06 01:10:46.013][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:46.302][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:46.304][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:46.305][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:46.306][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:46.908][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:46.910][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:46.913][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:46.915][rule$waitAsNeeded] Wait 0.0982459 second(s).
biodb.TRACE[2024-06-06 01:10:47.016][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:47.313][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:47.316][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:47.318][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:47.321][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:47.926][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:47.928][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:47.930][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:47.933][rule$waitAsNeeded] Wait 0.0827892 second(s).
biodb.TRACE[2024-06-06 01:10:48.022][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-06 01:10:48.322][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:48.324][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:48.325][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:48.327][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-06 01:10:48.913][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:48.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:48.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:48.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:48.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:48.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:48.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:48.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-06 01:10:48.940][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-06 01:10:48.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:48.947][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:48.949][rule$waitAsNeeded] Wait 0.0721161 second(s).
biodb.TRACE[2024-06-06 01:10:49.037][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:49.356][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:49.357][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:49.359][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:49.360][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:49.946][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:49.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:49.951][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:49.953][rule$waitAsNeeded] Wait 0.083045 second(s).
biodb.TRACE[2024-06-06 01:10:50.054][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:50.350][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:50.352][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:50.353][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:50.355][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:50.948][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:50.949][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:50.950][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:50.952][rule$waitAsNeeded] Wait 0.101417 second(s).
biodb.TRACE[2024-06-06 01:10:51.057][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:51.372][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:51.373][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:51.375][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:51.376][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:51.977][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:51.979][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:51.981][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:51.983][rule$waitAsNeeded] Wait 0.0730062 second(s).
biodb.TRACE[2024-06-06 01:10:52.061][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:52.376][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:52.377][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:52.378][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:52.380][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:52.974][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:52.975][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:52.977][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:52.978][rule$waitAsNeeded] Wait 0.082305 second(s).
biodb.TRACE[2024-06-06 01:10:53.067][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:53.368][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:53.370][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:53.371][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:53.373][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:53.961][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:53.963][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:53.964][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:53.965][rule$waitAsNeeded] Wait 0.101097 second(s).
biodb.TRACE[2024-06-06 01:10:54.070][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:54.364][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:54.366][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:54.367][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:54.369][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:54.980][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:54.982][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:54.983][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:54.985][rule$waitAsNeeded] Wait 0.0843821 second(s).
biodb.TRACE[2024-06-06 01:10:55.073][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:55.363][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:55.364][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:55.366][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:55.367][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:56.139][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:56.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:56.142][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-06 01:10:56.144][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:56.433][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:56.435][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:56.436][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:56.437][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:57.031][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:57.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:57.035][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:57.036][rule$waitAsNeeded] Wait 0.108086 second(s).
biodb.TRACE[2024-06-06 01:10:57.155][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:57.445][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:57.446][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:57.448][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:57.449][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:58.034][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-06 01:10:58.036][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-06 01:10:58.038][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-06 01:10:58.039][rule$waitAsNeeded] Wait 0.115899 second(s).
biodb.TRACE[2024-06-06 01:10:58.158][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-06 01:10:58.450][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-06 01:10:58.452][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-06 01:10:58.453][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-06 01:10:58.455][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-06 01:10:59.052][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-06 01:10:59.056][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2024-06-06 01:10:59.059][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-06 01:10:59.061][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-06 01:10:59.063][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-06 01:10:59.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:59.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:59.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:59.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:59.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:59.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:59.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:10:59.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:59.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:59.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.085][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:59.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:59.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:10:59.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:59.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:59.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:59.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:59.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:59.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:59.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:10:59.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:59.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:59.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.156][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:59.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-06 01:10:59.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-06 01:10:59.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-06 01:10:59.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-06 01:10:59.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-06 01:10:59.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-06 01:10:59.218][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-06 01:10:59.219][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-06 01:10:59.222][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-06 01:10:59.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:59.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:59.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:59.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:59.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:59.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:59.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:10:59.239][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-06-06 01:10:59.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-06 01:10:59.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:59.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:59.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:59.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:59.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:59.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-06 01:10:59.722][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-06-06 01:10:59.723][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-06 01:10:59.725][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-06 01:10:59.741][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-06 01:10:59.744][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-06 01:10:59.746][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-06 01:10:59.747][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-06 01:10:59.748][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-06 01:10:59.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-06 01:10:59.750][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-06 01:10:59.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-06 01:10:59.752][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-06 01:10:59.754][FUN] Functions in observer 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
LipidmapsStructureConn 3.96 2.45157.91
LipidmapsStructureEntry0.650.020.68