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This page was generated on 2024-05-22 11:35:27 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
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 / arm64see weekly results here

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: 2024-05-21 23:34:59 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 23:38:46 -0400 (Tue, 21 May 2024)
EllapsedTime: 227.3 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 3.79   1.88   56.39
* 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 [2024-05-21 23:36:47.505][biodb::testContext]
biodb.INFO [2024-05-21 23:36:47.508][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-21 23:36:47.510][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-21 23:36:47.513][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-21 23:36:47.515][biodb::testContext]
biodb.INFO [2024-05-21 23:36:47.527][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-21 23:36:47.531][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-21 23:36:47.542][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:36:47.544][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-21 23:36:47.545][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-21 23:36:47.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.551][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-21 23:36:47.594][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-21 23:36:47.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.599][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-21 23:36:47.601][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-21 23:36:47.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.605][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-21 23:36:47.607][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-21 23:36:47.608][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-21 23:36:47.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.612][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-21 23:36:47.614][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-21 23:36:47.615][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-21 23:36:47.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.620][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-21 23:36:47.621][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-21 23:36:47.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.626][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-21 23:36:47.627][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-21 23:36:47.628][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-21 23:36:47.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.633][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-21 23:36:47.634][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-21 23:36:47.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.638][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-21 23:36:47.640][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-21 23:36:47.641][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-21 23:36:47.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.646][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-21 23:36:47.647][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-21 23:36:47.648][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-21 23:36:47.649][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-21 23:36:47.651][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-21 23:36:47.652][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-21 23:36:47.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.657][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-21 23:36:47.658][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-21 23:36:47.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.663][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-21 23:36:47.664][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-21 23:36:47.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.667][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.DEBUG[2024-05-21 23:36:47.669][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-21 23:36:47.670][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-21 23:36:47.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.675][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-21 23:36:47.676][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-21 23:36:47.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.681][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-21 23:36:47.683][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-21 23:36:47.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.687][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-21 23:36:47.689][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-21 23:36:47.692][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-21 23:36:47.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.697][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-21 23:36:47.698][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-21 23:36:47.699][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-21 23:36:47.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.706][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-21 23:36:47.734][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.748][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-21 23:36:47.749][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:36:47.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.753][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.754][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.757][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:36:47.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:36:47.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.761][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-21 23:36:47.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:36:47.763][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.764][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.766][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:36:47.766][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:36:47.766][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-21 23:36:47.766][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-21 23:36:47.766][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-21 23:36:47.767][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:36:47.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:47.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:47.770][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:36:47.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:47.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:47.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.781][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.782][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:36:47.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:36:47.784][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.786][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.787][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-21 23:36:47.789][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.790][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-21 23:36:47.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:36:47.794][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.796][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.797][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.799][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-21 23:36:47.800][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:36:47.801][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.802][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-21 23:36:47.804][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:36:47.805][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.806][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.807][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:36:47.807][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:36:47.807][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-21 23:36:47.807][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-21 23:36:47.807][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-21 23:36:47.809][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:36:47.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:47.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:47.812][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:36:47.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:47.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:47.815][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.817][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.818][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:36:47.819][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:36:47.820][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.821][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.823][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-21 23:36:47.825][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.826][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-21 23:36:47.828][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:36:47.830][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.831][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.832][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.834][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.835][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:36:47.836][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:36:47.837][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.838][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-21 23:36:47.840][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:36:47.841][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.842][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.843][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.845][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:36:47.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:47.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:47.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:36:47.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:47.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:47.851][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.853][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.854][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:36:47.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:36:47.856][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.857][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.859][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-21 23:36:47.861][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.862][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-21 23:36:47.863][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:36:47.866][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.868][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.869][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.871][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-21 23:36:47.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:36:47.873][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.874][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-21 23:36:47.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:36:47.877][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.878][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:47.880][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.881][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:36:47.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:47.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:47.885][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:36:47.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:47.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:47.888][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:36:47.889][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.890][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:36:47.892][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:36:47.893][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:47.894][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:47.898][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:36:47.899][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.937][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[2024-05-21 23:36:47.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.954][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[2024-05-21 23:36:47.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:47.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:47.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:47.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:47.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:47.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.005][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-21 23:36:48.009][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-21 23:36:48.011][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-21 23:36:48.013][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-21 23:36:48.014][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-21 23:36:48.016][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-21 23:36:48.017][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-21 23:36:48.019][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-21 23:36:48.021][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-21 23:36:48.022][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-21 23:36:48.024][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-21 23:36:48.026][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-21 23:36:48.027][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-21 23:36:48.029][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-21 23:36:48.032][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-21 23:36:48.034][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-21 23:36:48.037][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-21 23:36:48.039][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-21 23:36:48.041][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-21 23:36:48.043][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-21 23:36:48.044][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-21 23:36:48.046][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-21 23:36:48.048][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-21 23:36:48.049][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-21 23:36:48.051][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-21 23:36:48.052][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-21 23:36:48.054][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-21 23:36:48.056][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-21 23:36:48.057][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-21 23:36:48.059][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-21 23:36:48.060][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-21 23:36:48.062][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-21 23:36:48.064][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-21 23:36:48.066][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-21 23:36:48.067][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-21 23:36:48.069][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-21 23:36:48.071][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-21 23:36:48.074][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-21 23:36:48.075][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-21 23:36:48.078][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-21 23:36:48.080][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-21 23:36:48.082][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-21 23:36:48.084][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-21 23:36:48.086][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-21 23:36:48.088][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-21 23:36:48.090][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-21 23:36:48.092][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-21 23:36:48.094][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-21 23:36:48.096][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-21 23:36:48.098][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-21 23:36:48.100][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-21 23:36:48.101][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-21 23:36:48.103][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-21 23:36:48.105][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-21 23:36:48.106][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-21 23:36:48.108][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-21 23:36:48.109][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-21 23:36:48.111][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-21 23:36:48.113][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-21 23:36:48.114][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-21 23:36:48.116][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-21 23:36:48.118][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-21 23:36:48.119][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-21 23:36:48.121][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-21 23:36:48.122][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-21 23:36:48.124][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-21 23:36:48.126][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-21 23:36:48.127][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-21 23:36:48.129][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-21 23:36:48.131][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-21 23:36:48.132][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-21 23:36:48.134][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-21 23:36:48.135][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-21 23:36:48.137][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-21 23:36:48.139][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-21 23:36:48.140][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-21 23:36:48.142][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-21 23:36:48.144][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-21 23:36:48.145][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-21 23:36:48.148][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-21 23:36:48.149][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-21 23:36:48.151][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-21 23:36:48.153][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-21 23:36:48.190][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-21 23:36:48.193][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-21 23:36:48.196][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:36:48.197][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.200][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.201][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[2024-05-21 23:36:48.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.260][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[2024-05-21 23:36:48.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.289][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[2024-05-21 23:36:48.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.302][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[2024-05-21 23:36:48.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.315][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[2024-05-21 23:36:48.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:36:48.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:36:48.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.383][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[2024-05-21 23:36:48.386][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-21 23:36:48.396][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:36:48.398][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:48.399][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-21 23:36:48.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:48.402][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:36:48.403][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:48.405][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:36:48.406][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:48.407][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:36:48.408][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:36:48.410][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:36:48.411][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:48.412][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-21 23:36:48.413][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-21 23:36:48.414][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-21 23:36:48.416][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-21 23:36:48.417][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:36:48.417][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:36:48.419][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:36:48.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:48.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:48.422][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:36:48.424][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:36:48.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:36:48.427][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:36:48.428][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-21 23:36:48.428][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-21 23:36:48.430][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:36:48.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:36:48.432][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-21 23:36:48.433][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:36:48.439][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-21 23:36:48.441][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-21 23:36:48.466][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:36:48.468][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-21 23:36:48.472][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:36:48.476][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-21 23:36:48.480][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-21 23:36:48.482][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-21 23:36:48.483][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-21 23:36:48.485][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-21 23:36:48.496][biodb::testThat]
biodb.INFO [2024-05-21 23:36:48.498][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-21 23:36:48.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:48.501][biodb::testThat]
biodb.TRACE[2024-05-21 23:36:48.508][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[2024-05-21 23:36:48.510][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-21 23:36:48.522][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-21 23:36:48.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:36:48.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:48.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:48.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:48.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:48.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:48.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:36:48.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-21 23:36:48.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-21 23:36:48.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.627][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-21 23:36:48.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-21 23:36:48.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.636][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-21 23:36:48.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-21 23:36:48.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.644][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:48.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:48.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.677][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:48.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:48.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:48.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:48.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:48.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:48.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.693][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-21 23:36:48.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:48.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.698][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-21 23:36:48.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:48.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.703][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:48.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:48.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:48.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:48.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.725][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-21 23:36:48.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.730][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-21 23:36:48.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.787][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-21 23:36:48.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:48.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:48.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:48.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:48.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.866][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:48.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:48.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.880][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:48.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:48.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:48.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:48.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:36:48.919][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-21 23:36:48.941][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-21 23:36:48.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-21 23:36:48.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.948][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-21 23:36:48.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-21 23:36:48.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.960][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-21 23:36:48.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-21 23:36:48.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.966][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-21 23:36:48.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-21 23:36:48.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:48.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:48.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.025][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:49.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:49.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.110][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:49.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:49.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.116][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:49.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:49.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.121][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:49.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:49.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.211][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.213][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.216][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.280][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.282][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.285][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.339][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.351][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.352][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.355][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.393][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:49.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:49.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:49.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:49.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.405][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:49.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:49.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.410][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:49.413][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:49.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.417][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.419][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:49.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:49.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.474][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.517][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.535][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.540][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.541][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.544][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.578][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.581][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.585][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.602][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.604][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.610][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.623][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:49.626][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:49.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.630][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.643][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.655][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.660][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.679][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.680][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.684][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.703][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.706][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.710][ef$get] fields variable is a list.
biodb.INFO [2024-05-21 23:36:49.742][biodb::testThat]
biodb.INFO [2024-05-21 23:36:49.743][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-21 23:36:49.745][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:49.748][biodb::testThat]
biodb.DEBUG[2024-05-21 23:36:49.763][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-05-21 23:36:49.772][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-21 23:36:49.782][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-05-21 23:36:49.786][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-21 23:36:49.792][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-05-21 23:36:49.795][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-21 23:36:49.835][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-21 23:36:49.838][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-21 23:36:49.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:36:49.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:36:49.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:36:49.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:36:49.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:36:49.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:36:49.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:36:49.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:49.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:49.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-21 23:36:49.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-21 23:36:49.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-21 23:36:49.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-21 23:36:49.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.889][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-21 23:36:49.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-21 23:36:49.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.895][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-21 23:36:49.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-21 23:36:49.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.902][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.908][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:36:49.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.914][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.925][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:36:49.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.931][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-21 23:36:49.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.936][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-21 23:36:49.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:49.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:49.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:49.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:36:49.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:36:49.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.964][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-21 23:36:49.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.969][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-21 23:36:49.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.986][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-21 23:36:49.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:49.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:49.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:49.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:49.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:50.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:50.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:50.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:50.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:50.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:50.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:50.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.019][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:50.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:50.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.024][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:50.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:50.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:50.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:50.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.035][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:50.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:36:50.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:50.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:50.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:50.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:50.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:50.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:50.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:50.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:50.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:50.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:36:50.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:36:50.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:36:50.836][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-21 23:36:50.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-21 23:36:50.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-21 23:36:50.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-21 23:36:50.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-21 23:36:50.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-21 23:36:50.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-21 23:36:50.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-21 23:36:50.866][biodb::testThat]
biodb.INFO [2024-05-21 23:36:50.868][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-21 23:36:50.869][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:50.870][biodb::testThat]
biodb.TRACE[2024-05-21 23:36:50.880][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:50.881][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:50.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.883][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:36:50.885][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-05-21 23:36:50.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:50.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:50.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:50.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:50.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:50.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:50.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:50.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:50.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:36:50.941][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-21 23:36:50.946][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-21 23:36:50.966][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:36:50.968][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:36:50.970][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-05-21 23:36:51.802][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride does not exist.
biodb.TRACE[2024-05-21 23:36:51.803][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:36:51.809][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:36:51.811][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-05-21 23:36:52.410][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:36:52.415][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-05-21 23:36:52.443][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-05-21 23:36:52.447][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-05-21 23:36:52.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:52.491][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:52.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.496][ef$get] fields variable is a list.
biodb.INFO [2024-05-21 23:36:52.508][biodb::testThat]
biodb.INFO [2024-05-21 23:36:52.519][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-21 23:36:52.522][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:52.524][biodb::testThat]
biodb.TRACE[2024-05-21 23:36:52.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:52.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:52.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:52.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:52.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:52.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:52.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:36:52.728][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-21 23:36:52.733][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-21 23:36:52.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-21 23:36:52.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-21 23:36:52.753][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-05-21 23:36:52.811][biodb::testThat]
biodb.INFO [2024-05-21 23:36:52.814][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-21 23:36:52.816][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:52.819][biodb::testThat]
biodb.TRACE[2024-05-21 23:36:52.857][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-21 23:36:52.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-21 23:36:52.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.865][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-21 23:36:52.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-21 23:36:52.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-21 23:36:52.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-21 23:36:52.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-21 23:36:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-21 23:36:52.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-21 23:36:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-21 23:36:52.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.934][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-21 23:36:52.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-21 23:36:52.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.941][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-21 23:36:52.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-21 23:36:52.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:52.949][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-21 23:36:52.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-21 23:36:52.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:52.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-21 23:36:52.978][biodb::testThat]
biodb.INFO [2024-05-21 23:36:52.980][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-21 23:36:52.981][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:52.983][biodb::testThat]
biodb.INFO [2024-05-21 23:36:53.004][biodb::testThat]
biodb.INFO [2024-05-21 23:36:53.005][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-21 23:36:53.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:53.008][biodb::testThat]
biodb.INFO [2024-05-21 23:36:53.022][biodb::testThat]
biodb.INFO [2024-05-21 23:36:53.023][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-21 23:36:53.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:53.026][biodb::testThat]
biodb.DEBUG[2024-05-21 23:36:53.031][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-05-21 23:36:53.324][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-05-21 23:36:54.123][biodb::testThat]
biodb.INFO [2024-05-21 23:36:54.125][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-21 23:36:54.127][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:54.129][biodb::testThat]
biodb.TRACE[2024-05-21 23:36:54.164][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:54.166][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:54.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.170][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.172][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.173][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.176][ef$get] fields variable is a list.
biodb.INFO [2024-05-21 23:36:54.178][biodb::testThat]
biodb.INFO [2024-05-21 23:36:54.179][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-21 23:36:54.181][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:36:54.182][biodb::testThat]
biodb.TRACE[2024-05-21 23:36:54.204][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:54.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:54.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:54.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:54.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:36:54.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:36:54.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:36:54.330][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-21 23:36:54.334][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-21 23:36:54.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-21 23:36:54.339][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-21 23:36:54.341][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-21 23:36:54.443][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-21 23:36:54.447][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-21 23:36:54.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-21 23:36:54.451][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-21 23:36:54.453][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-05-21 23:36:54.474][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-21 23:36:54.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-21 23:36:54.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-21 23:36:54.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-21 23:36:54.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:36:54.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:36:54.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:36:54.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:36:54.565][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-21 23:36:54.583][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:36:54.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:36:54.600][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-21 23:36:54.888][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[2024-05-21 23:36:54.889][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:36:54.892][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[2024-05-21 23:36:54.895][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[2024-05-21 23:37:00.304][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:37:00.307][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-05-21 23:37:00.475][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-05-21 23:37:02.578][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-21 23:37:02.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:02.583][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:37:02.586][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-21 23:37:02.870][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-05-21 23:37:02.871][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:02.874][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:02.876][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-05-21 23:37:03.464][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:37:03.469][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-05-21 23:37:03.477][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-05-21 23:37:03.544][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-05-21 23:37:03.548][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:03.550][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:03.552][rule$waitAsNeeded] Wait 0.0331089 second(s).
biodb.TRACE[2024-05-21 23:37:03.588][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-05-21 23:37:03.876][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06 does not exist.
biodb.TRACE[2024-05-21 23:37:03.877][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:03.880][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:03.882][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-05-21 23:37:04.668][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:37:04.672][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-05-21 23:37:04.681][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-05-21 23:37:04.738][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-21 23:37:04.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-21 23:37:04.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:04.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-21 23:37:04.779][biodb::testThat]
biodb.INFO [2024-05-21 23:37:04.780][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-21 23:37:04.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:37:04.783][biodb::testThat]
biodb.TRACE[2024-05-21 23:37:04.787][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-21 23:37:04.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-21 23:37:04.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:04.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:04.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-21 23:37:04.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-21 23:37:04.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:04.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:04.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:04.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:04.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:04.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:04.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:04.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:04.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:04.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:04.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:04.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:04.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:04.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:04.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:04.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:04.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:04.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:37:04.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:04.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:04.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:04.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:04.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:04.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:04.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:37:04.851][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-21 23:37:04.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:04.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:37:04.861][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-05-21 23:37:05.144][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[2024-05-21 23:37:05.146][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:05.148][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[2024-05-21 23:37:05.151][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[2024-05-21 23:37:10.577][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:37:10.582][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-05-21 23:37:10.732][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-05-21 23:37:13.019][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-05-21 23:37:13.060][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-21 23:37:13.063][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-05-21 23:37:13.066][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-05-21 23:37:13.081][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-05-21 23:37:13.084][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-21 23:37:13.086][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-21 23:37:13.087][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-21 23:37:13.089][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-21 23:37:13.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:13.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:13.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:13.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:13.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:13.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:13.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:37:13.125][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-05-21 23:37:13.129][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:13.131][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:37:13.133][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-05-21 23:37:13.428][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:13.430][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:13.432][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[2024-05-21 23:37:13.435][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-05-21 23:37:14.037][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:37:14.041][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-05-21 23:37:14.047][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-05-21 23:37:14.052][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-05-21 23:37:14.054][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-21 23:37:14.056][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-21 23:37:14.058][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-21 23:37:14.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:14.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:14.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:14.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:14.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:14.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:14.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:14.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-21 23:37:14.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-21 23:37:14.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-21 23:37:14.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-21 23:37:14.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.119][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-21 23:37:14.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-21 23:37:14.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.124][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-21 23:37:14.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-21 23:37:14.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.129][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:37:14.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:37:14.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.135][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:37:14.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:37:14.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.141][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:37:14.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:37:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:37:14.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:37:14.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.156][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-21 23:37:14.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:14.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.165][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-21 23:37:14.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:14.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:37:14.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:37:14.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:37:14.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:37:14.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:37:14.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:37:14.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.203][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-21 23:37:14.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.208][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-21 23:37:14.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:37:14.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:37:14.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.226][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-21 23:37:14.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.232][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.239][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.251][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:37:14.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:14.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:14.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:14.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:14.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:14.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:14.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:14.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-21 23:37:14.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-21 23:37:14.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.324][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-21 23:37:14.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-21 23:37:14.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.330][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-21 23:37:14.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-21 23:37:14.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.336][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:37:14.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:37:14.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.343][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:37:14.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-21 23:37:14.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.350][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:37:14.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:37:14.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:37:14.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-21 23:37:14.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.363][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-21 23:37:14.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:14.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.370][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-21 23:37:14.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:14.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.377][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:37:14.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:37:14.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-21 23:37:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-21 23:37:14.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:37:14.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:37:14.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.401][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-21 23:37:14.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.408][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-21 23:37:14.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:37:14.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:37:14.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.478][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-21 23:37:14.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:37:14.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.488][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.496][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.512][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:14.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:14.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:37:14.589][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-05-21 23:37:14.598][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-21 23:37:14.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:14.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:14.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:14.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:14.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:14.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:14.614][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.TRACE[2024-05-21 23:37:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.620][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.625][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.627][private$selectFields]
biodb.TRACE[2024-05-21 23:37:14.628][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:14.629][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:14.630][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.632][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.633][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.635][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.636][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.638][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.640][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.642][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.643][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.644][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.645][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.648][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.649][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:14.650][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.655][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.660][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.675][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-21 23:37:14.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:14.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:14.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:14.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:14.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:14.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:14.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.832][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.837][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.838][private$selectFields]
biodb.TRACE[2024-05-21 23:37:14.839][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:14.841][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:14.842][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.843][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.848][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.850][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.852][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.853][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.854][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.856][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.857][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.859][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.861][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:14.862][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.867][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.872][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.877][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-21 23:37:14.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:14.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:14.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:14.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:14.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:14.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:14.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:14.975][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.982][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:14.988][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.989][private$selectFields]
biodb.TRACE[2024-05-21 23:37:14.990][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:14.991][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:14.993][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:14.994][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.996][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:14.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:14.998][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.000][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.001][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.004][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.006][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:15.008][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:15.010][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.012][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.016][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.018][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:15.020][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.036][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:15.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.044][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-21 23:37:15.046][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-21 23:37:15.048][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-21 23:37:15.076][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-21 23:37:15.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-21 23:37:15.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-21 23:37:15.100][biodb::testThat]
biodb.INFO [2024-05-21 23:37:15.101][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-21 23:37:15.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:37:15.105][biodb::testThat]
biodb.TRACE[2024-05-21 23:37:15.109][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-21 23:37:15.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-21 23:37:15.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-21 23:37:15.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-21 23:37:15.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:15.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:15.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:15.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:15.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:15.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:15.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:15.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:15.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:15.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:15.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:37:15.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:15.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:15.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:15.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:15.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:15.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:15.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:37:15.261][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-05-21 23:37:15.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:15.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:37:15.270][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-05-21 23:37:15.565][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375 does not exist.
biodb.TRACE[2024-05-21 23:37:15.568][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:15.571][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:15.574][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-05-21 23:37:20.890][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:37:20.893][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-05-21 23:37:20.998][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-05-21 23:37:22.522][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-21 23:37:22.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:22.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:22.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:22.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:22.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:22.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:22.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:22.594][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.600][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.623][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.624][private$selectFields]
biodb.TRACE[2024-05-21 23:37:22.625][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:22.627][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:22.628][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.629][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.631][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.633][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.634][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.636][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.638][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.639][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.649][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.651][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.652][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.655][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.656][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:22.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.662][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.667][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.673][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-21 23:37:22.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:22.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:22.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:22.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:22.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:22.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:22.697][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.TRACE[2024-05-21 23:37:22.698][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.704][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.709][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.710][private$selectFields]
biodb.TRACE[2024-05-21 23:37:22.712][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:22.713][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:22.714][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.716][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.717][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.720][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.722][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.723][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.726][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.727][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.728][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.730][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.731][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.733][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.735][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:22.736][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.741][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.747][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.755][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-21 23:37:22.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:22.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:22.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:22.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:22.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:22.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:22.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:22.884][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.893][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.901][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.903][private$selectFields]
biodb.TRACE[2024-05-21 23:37:22.905][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:22.907][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:22.909][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.911][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.914][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.917][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.919][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.922][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.926][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.928][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.930][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:22.932][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.934][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.938][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.940][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:22.942][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.951][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.959][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:22.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:22.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:22.968][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-21 23:37:22.970][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-21 23:37:22.972][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-21 23:37:23.008][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-21 23:37:23.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-21 23:37:23.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:23.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-21 23:37:23.037][biodb::testThat]
biodb.INFO [2024-05-21 23:37:23.039][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-21 23:37:23.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:37:23.042][biodb::testThat]
biodb.TRACE[2024-05-21 23:37:23.046][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-21 23:37:23.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-21 23:37:23.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:23.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:23.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-21 23:37:23.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-21 23:37:23.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:23.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:23.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:23.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:23.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:23.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:23.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:23.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:23.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:23.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:23.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:23.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:23.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:23.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:23.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:37:23.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:23.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:37:23.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:23.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:23.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:23.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:23.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:23.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:23.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:37:23.110][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-21 23:37:23.113][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-21 23:37:23.116][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-21 23:37:23.118][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-21 23:37:23.260][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-21 23:37:24.920][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-21 23:37:24.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:24.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:24.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:25.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:25.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:25.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:25.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:25.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.068][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.073][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.074][private$selectFields]
biodb.TRACE[2024-05-21 23:37:25.075][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:25.076][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:25.077][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.079][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.080][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.082][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.083][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.085][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.087][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.088][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.090][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.091][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.092][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.095][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.096][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:25.097][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.102][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.107][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.114][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-21 23:37:25.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:25.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:25.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:25.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:25.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:25.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:25.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:25.132][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.137][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.142][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.143][private$selectFields]
biodb.TRACE[2024-05-21 23:37:25.144][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:25.145][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:25.147][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.148][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.149][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.152][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.153][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.154][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.157][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.158][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.159][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.160][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.162][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.164][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.165][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:25.167][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.172][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.177][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.182][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-21 23:37:25.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:25.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:25.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:25.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:25.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:25.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:25.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:25.198][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.205][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.213][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.215][private$selectFields]
biodb.TRACE[2024-05-21 23:37:25.216][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-21 23:37:25.217][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-21 23:37:25.219][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.220][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.222][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.224][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.226][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.227][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.231][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.233][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.235][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-21 23:37:25.236][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.238][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.240][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.241][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-21 23:37:25.243][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.248][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.254][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:25.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:25.259][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-21 23:37:25.260][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-21 23:37:25.262][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-21 23:37:25.307][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-21 23:37:25.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-21 23:37:25.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:25.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-21 23:37:25.322][biodb::testThat]
biodb.INFO [2024-05-21 23:37:25.324][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-21 23:37:25.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:37:25.327][biodb::testThat]
biodb.DEBUG[2024-05-21 23:37:25.330][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-21 23:37:25.332][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-21 23:37:25.334][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-21 23:37:25.335][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-21 23:37:25.337][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-21 23:37:25.340][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-21 23:37:25.341][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-21 23:37:25.343][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-21 23:37:25.344][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-21 23:37:25.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:25.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:25.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:25.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:25.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:25.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:25.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:37:25.404][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-05-21 23:37:25.408][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:25.409][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:37:25.411][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:25.704][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:25.706][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:25.709][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:25.711][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:26.293][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:26.296][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:26.298][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:26.300][rule$waitAsNeeded] Wait 0.111196 second(s).
biodb.TRACE[2024-05-21 23:37:26.416][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:26.712][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:26.713][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:26.715][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:26.716][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:27.309][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:27.312][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:27.314][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:27.316][rule$waitAsNeeded] Wait 0.0992949 second(s).
biodb.TRACE[2024-05-21 23:37:27.432][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:27.728][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:27.729][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:27.731][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:27.732][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:28.324][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:28.326][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:28.327][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:28.328][rule$waitAsNeeded] Wait 0.102991 second(s).
biodb.TRACE[2024-05-21 23:37:28.448][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:28.736][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:28.737][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:28.739][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:28.741][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:29.327][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:29.330][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:29.332][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:29.335][rule$waitAsNeeded] Wait 0.112952 second(s).
biodb.TRACE[2024-05-21 23:37:29.452][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:29.747][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:29.749][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:29.751][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:29.752][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:30.346][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:30.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:30.351][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:30.353][rule$waitAsNeeded] Wait 0.0982561 second(s).
biodb.TRACE[2024-05-21 23:37:30.453][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:30.746][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:30.748][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:30.750][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:30.752][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:31.347][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:31.349][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:31.353][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:31.355][rule$waitAsNeeded] Wait 0.0977859 second(s).
biodb.TRACE[2024-05-21 23:37:31.470][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:31.756][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:31.758][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:31.759][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:31.760][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:32.373][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:32.377][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:32.380][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:32.382][rule$waitAsNeeded] Wait 0.0872982 second(s).
biodb.TRACE[2024-05-21 23:37:32.486][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:32.772][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:32.775][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:32.777][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:32.780][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:33.363][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:33.366][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:33.368][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:33.370][rule$waitAsNeeded] Wait 0.115217 second(s).
biodb.TRACE[2024-05-21 23:37:33.502][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:33.794][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:33.796][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:33.798][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:33.801][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:34.395][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:34.397][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:34.400][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:34.402][rule$waitAsNeeded] Wait 0.099489 second(s).
biodb.TRACE[2024-05-21 23:37:34.518][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-21 23:37:34.815][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:34.817][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:34.820][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:34.821][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-21 23:37:35.411][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.INFO [2024-05-21 23:37:35.415][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-05-21 23:37:35.419][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-05-21 23:37:35.423][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-21 23:37:35.425][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-21 23:37:35.428][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-21 23:37:35.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:35.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:35.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:35.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:35.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:35.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:35.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:35.455][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:35.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:35.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:35.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:35.463][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:35.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:35.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:35.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:35.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:35.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:35.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:35.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:35.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:35.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:35.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:35.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:35.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:35.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:35.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:35.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:35.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:35.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:35.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:35.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:35.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:35.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:35.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:35.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:35.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:35.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:35.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:35.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:37:35.520][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-21 23:37:35.522][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-21 23:37:35.553][biodb::testThat]
biodb.INFO [2024-05-21 23:37:35.555][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-21 23:37:35.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:37:35.559][biodb::testThat]
biodb.DEBUG[2024-05-21 23:37:35.576][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-05-21 23:37:35.578][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-05-21 23:37:35.579][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-21 23:37:35.581][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-05-21 23:37:35.583][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-21 23:37:35.584][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-21 23:37:35.586][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-21 23:37:35.587][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-21 23:37:35.588][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-21 23:37:35.590][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-21 23:37:35.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:35.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:35.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:35.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:35.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:35.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:35.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:37:35.610][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-05-21 23:37:35.614][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:35.615][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:37:35.617][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:35.903][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:35.904][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:35.906][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:35.907][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:36.490][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:36.492][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:36.494][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:36.497][rule$waitAsNeeded] Wait 0.120107 second(s).
biodb.TRACE[2024-05-21 23:37:36.629][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:36.917][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:36.918][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:36.920][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:36.921][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:37.505][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:37.506][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:37.507][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:37.509][rule$waitAsNeeded] Wait 0.118675 second(s).
biodb.TRACE[2024-05-21 23:37:37.644][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:37.928][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:37.930][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:37.931][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:37.933][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:38.522][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:38.524][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:38.526][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:38.529][rule$waitAsNeeded] Wait 0.115469 second(s).
biodb.TRACE[2024-05-21 23:37:38.661][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:38.956][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:38.959][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:38.961][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:38.963][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:39.558][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:39.560][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:39.561][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:39.563][rule$waitAsNeeded] Wait 0.0972869 second(s).
biodb.TRACE[2024-05-21 23:37:39.676][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:39.971][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:39.973][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:39.975][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:39.978][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:40.570][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:40.572][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:40.574][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:40.577][rule$waitAsNeeded] Wait 0.0996749 second(s).
biodb.TRACE[2024-05-21 23:37:40.692][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:40.988][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:40.990][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:40.991][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:40.992][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:41.586][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:41.588][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:41.590][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:41.592][rule$waitAsNeeded] Wait 0.100522 second(s).
biodb.TRACE[2024-05-21 23:37:41.709][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:42.003][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:42.005][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:42.007][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:42.010][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:42.602][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:42.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:42.606][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:42.608][rule$waitAsNeeded] Wait 0.100626 second(s).
biodb.TRACE[2024-05-21 23:37:42.725][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:43.013][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:43.014][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:43.016][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:43.017][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:43.602][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:43.605][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:43.607][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:43.609][rule$waitAsNeeded] Wait 0.115512 second(s).
biodb.TRACE[2024-05-21 23:37:43.741][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:44.028][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:44.029][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:44.031][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:44.032][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:44.619][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:44.621][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:44.623][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:44.626][rule$waitAsNeeded] Wait 0.115247 second(s).
biodb.TRACE[2024-05-21 23:37:44.757][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-21 23:37:45.059][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:45.061][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:45.064][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:45.067][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-21 23:37:45.650][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:45.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:45.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:45.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:45.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:45.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:45.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:45.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:37:45.678][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-05-21 23:37:45.682][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:45.683][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:45.685][rule$waitAsNeeded] Wait 0.071506 second(s).
biodb.TRACE[2024-05-21 23:37:45.774][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:46.065][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:46.067][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:46.070][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:46.072][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:46.528][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:46.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:46.531][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:46.532][rule$waitAsNeeded] Wait 0.240995 second(s).
biodb.TRACE[2024-05-21 23:37:46.778][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:47.065][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:47.067][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:47.068][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:47.070][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:47.656][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:47.658][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:47.659][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:47.661][rule$waitAsNeeded] Wait 0.116805 second(s).
biodb.TRACE[2024-05-21 23:37:47.780][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:48.069][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:48.071][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:48.072][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:48.073][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:48.657][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:48.659][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:48.661][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:48.663][rule$waitAsNeeded] Wait 0.116567 second(s).
biodb.TRACE[2024-05-21 23:37:48.797][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:49.084][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:49.087][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:49.089][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:49.092][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:49.673][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:49.676][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:49.678][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:49.680][rule$waitAsNeeded] Wait 0.115727 second(s).
biodb.TRACE[2024-05-21 23:37:49.813][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:50.106][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:50.109][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:50.111][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:50.113][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:50.705][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:50.708][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:50.710][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:50.713][rule$waitAsNeeded] Wait 0.0994549 second(s).
biodb.TRACE[2024-05-21 23:37:50.829][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:51.124][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:51.126][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:51.129][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:51.131][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:51.712][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:51.714][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:51.717][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:51.719][rule$waitAsNeeded] Wait 0.108684 second(s).
biodb.TRACE[2024-05-21 23:37:51.835][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:52.131][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:52.132][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:52.134][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:52.135][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:52.728][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:52.753][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:52.760][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:52.763][rule$waitAsNeeded] Wait 0.0717881 second(s).
biodb.TRACE[2024-05-21 23:37:52.851][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:53.140][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:53.142][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:53.145][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:53.147][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:53.744][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:53.745][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:53.747][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:53.749][rule$waitAsNeeded] Wait 0.101895 second(s).
biodb.TRACE[2024-05-21 23:37:53.867][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:54.152][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:54.153][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:54.155][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:54.156][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:54.744][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:37:54.747][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:54.749][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:37:54.751][rule$waitAsNeeded] Wait 0.115887 second(s).
biodb.TRACE[2024-05-21 23:37:54.883][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-21 23:37:55.178][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:37:55.180][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:55.182][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:37:55.184][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-21 23:37:55.777][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-21 23:37:55.784][private$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[2024-05-21 23:37:55.790][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-21 23:37:55.794][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-21 23:37:55.797][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-21 23:37:55.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:55.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:55.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:55.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:55.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:55.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:55.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:55.831][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:55.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:55.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.839][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:55.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:55.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:37:55.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:37:55.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:37:55.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:37:55.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:37:55.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:37:55.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:37:55.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:37:55.886][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:55.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:55.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.894][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:55.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:37:55.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:37:55.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:37:55.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:37:55.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:37:55.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:37:55.984][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-21 23:37:55.986][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-21 23:37:55.987][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-05-21 23:37:56.425][biodb::testThat]
biodb.INFO [2024-05-21 23:37:56.427][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-21 23:37:56.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:37:56.432][biodb::testThat]
biodb.INFO [2024-05-21 23:37:56.538][biodb::testThat]
biodb.INFO [2024-05-21 23:37:56.541][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-21 23:37:56.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:37:56.545][biodb::testThat]
biodb.INFO [2024-05-21 23:37:56.581][biodb::testThat]
biodb.INFO [2024-05-21 23:37:56.612][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-21 23:37:56.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:37:56.618][biodb::testThat]
biodb.DEBUG[2024-05-21 23:37:56.624][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-21 23:37:56.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:37:56.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:37:56.633][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-05-21 23:37:56.928][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV does not exist.
biodb.TRACE[2024-05-21 23:37:56.929][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:37:56.931][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[2024-05-21 23:37:56.933][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-05-21 23:38:02.377][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:38:02.380][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-05-21 23:38:02.518][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-05-21 23:38:04.453][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-21 23:38:04.455][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-21 23:38:04.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:04.457][ef$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:04.459][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:38:04.460][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-21 23:38:04.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:04.462][ef$get] fields variable is a list.
biodb.INFO [2024-05-21 23:38:04.465][biodb::testThat]
biodb.INFO [2024-05-21 23:38:04.466][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-21 23:38:04.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:38:04.468][biodb::testThat]
biodb.ERROR[2024-05-21 23:38:04.492][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-21 23:38:04.511][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-21 23:38:04.541][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-21 23:38:04.542][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-21 23:38:04.544][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-21 23:38:04.545][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-21 23:38:04.546][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:04.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:04.548][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.551][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-21 23:38:04.565][biodb::testContext]
biodb.INFO [2024-05-21 23:38:04.567][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-21 23:38:04.568][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-05-21 23:38:04.569][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-21 23:38:04.570][biodb::testContext]
biodb.INFO [2024-05-21 23:38:04.573][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-21 23:38:04.576][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-21 23:38:04.582][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:38:04.583][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-21 23:38:04.584][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-21 23:38:04.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.589][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-21 23:38:04.591][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-21 23:38:04.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.597][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-21 23:38:04.598][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-21 23:38:04.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.603][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-21 23:38:04.605][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-21 23:38:04.606][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-21 23:38:04.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.611][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-21 23:38:04.612][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-21 23:38:04.613][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-21 23:38:04.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.618][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-21 23:38:04.619][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-21 23:38:04.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.624][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-21 23:38:04.626][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-21 23:38:04.627][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-21 23:38:04.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.632][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-21 23:38:04.633][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-21 23:38:04.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.636][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.DEBUG[2024-05-21 23:38:04.637][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-21 23:38:04.639][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-21 23:38:04.640][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-21 23:38:04.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.647][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-21 23:38:04.649][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-21 23:38:04.650][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-21 23:38:04.651][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-21 23:38:04.652][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-21 23:38:04.654][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-21 23:38:04.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.659][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-21 23:38:04.660][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-21 23:38:04.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.665][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-21 23:38:04.666][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-21 23:38:04.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.674][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-21 23:38:04.676][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-21 23:38:04.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.681][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-21 23:38:04.682][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-21 23:38:04.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.687][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-21 23:38:04.688][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-21 23:38:04.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.693][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-21 23:38:04.694][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-21 23:38:04.698][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-21 23:38:04.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.703][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-21 23:38:04.704][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-21 23:38:04.706][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-21 23:38:04.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.711][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-21 23:38:04.714][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.716][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-21 23:38:04.718][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.720][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:04.723][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.725][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.726][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.729][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:38:04.731][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:04.732][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.733][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-21 23:38:04.734][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:04.735][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.737][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.739][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:38:04.739][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:38:04.739][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-21 23:38:04.739][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-21 23:38:04.739][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-21 23:38:04.740][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:04.742][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:04.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:04.744][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:04.745][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:04.746][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:04.748][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.749][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.750][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:04.751][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:04.753][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.754][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.756][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-21 23:38:04.759][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.762][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-21 23:38:04.764][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.766][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:04.768][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.770][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.772][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.774][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.776][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-21 23:38:04.779][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:04.781][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.782][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-21 23:38:04.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:04.785][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.786][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.787][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:38:04.787][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:38:04.787][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-21 23:38:04.787][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-21 23:38:04.787][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-21 23:38:04.789][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:04.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:04.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:04.792][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:04.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:04.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:04.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.797][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:04.799][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:04.802][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.803][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.805][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-21 23:38:04.807][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.808][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-21 23:38:04.809][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.811][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:04.812][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.813][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.814][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.816][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.817][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:38:04.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:04.819][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.821][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-21 23:38:04.822][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:04.823][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.824][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.826][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.827][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:04.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:04.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:04.830][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:04.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:04.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:04.834][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.836][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.837][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:04.838][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:04.839][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.853][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.855][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-21 23:38:04.858][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.859][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-21 23:38:04.860][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.861][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:04.863][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.864][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.865][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.866][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.867][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-21 23:38:04.869][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:04.870][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.871][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-21 23:38:04.872][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:04.873][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.875][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:04.876][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.877][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:04.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:04.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:04.881][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:04.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:04.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:04.884][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:04.885][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.886][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:04.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:04.889][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:04.890][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:04.891][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:38:04.893][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.945][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[2024-05-21 23:38:04.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:04.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:04.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:04.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:04.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:04.992][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-21 23:38:04.993][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-21 23:38:04.995][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-21 23:38:04.997][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-21 23:38:04.998][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-21 23:38:05.000][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-21 23:38:05.001][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-21 23:38:05.003][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-21 23:38:05.004][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-21 23:38:05.006][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-21 23:38:05.008][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-21 23:38:05.009][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-21 23:38:05.011][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-21 23:38:05.013][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-21 23:38:05.014][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-21 23:38:05.016][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-21 23:38:05.017][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-21 23:38:05.019][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-21 23:38:05.021][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-21 23:38:05.022][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-21 23:38:05.024][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-21 23:38:05.026][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-21 23:38:05.027][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-21 23:38:05.029][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-21 23:38:05.030][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-21 23:38:05.032][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-21 23:38:05.033][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-21 23:38:05.035][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-21 23:38:05.036][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-21 23:38:05.039][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-21 23:38:05.042][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-21 23:38:05.046][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-21 23:38:05.048][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-21 23:38:05.051][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-21 23:38:05.052][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-21 23:38:05.055][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-21 23:38:05.058][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-21 23:38:05.061][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-21 23:38:05.063][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-21 23:38:05.066][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-21 23:38:05.068][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-21 23:38:05.069][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-21 23:38:05.071][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-21 23:38:05.073][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-21 23:38:05.075][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-21 23:38:05.076][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-21 23:38:05.078][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-21 23:38:05.080][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-21 23:38:05.081][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-21 23:38:05.083][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-21 23:38:05.085][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-21 23:38:05.087][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-21 23:38:05.089][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-21 23:38:05.091][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-21 23:38:05.092][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-21 23:38:05.094][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-21 23:38:05.096][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-21 23:38:05.098][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-21 23:38:05.100][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-21 23:38:05.102][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-21 23:38:05.104][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-21 23:38:05.105][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-21 23:38:05.107][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-21 23:38:05.108][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-21 23:38:05.110][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-21 23:38:05.111][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-21 23:38:05.113][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-21 23:38:05.115][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-21 23:38:05.116][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-21 23:38:05.118][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-21 23:38:05.119][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-21 23:38:05.121][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-21 23:38:05.122][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-21 23:38:05.124][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-21 23:38:05.126][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-21 23:38:05.127][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-21 23:38:05.129][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-21 23:38:05.130][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-21 23:38:05.132][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-21 23:38:05.134][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-21 23:38:05.136][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-21 23:38:05.139][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-21 23:38:05.141][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-21 23:38:05.144][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-21 23:38:05.148][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-21 23:38:05.149][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:38:05.150][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.153][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.154][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[2024-05-21 23:38:05.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.221][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[2024-05-21 23:38:05.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.233][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[2024-05-21 23:38:05.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.280][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[2024-05-21 23:38:05.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:05.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:05.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:05.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:05.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:05.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:05.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:05.355][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-21 23:38:05.357][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:38:05.359][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:05.361][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-21 23:38:05.362][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:05.364][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:05.365][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:05.366][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:05.367][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:05.369][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:05.371][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:38:05.372][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:05.373][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:05.375][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-21 23:38:05.376][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-21 23:38:05.378][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-21 23:38:05.379][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:05.380][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:38:05.380][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:38:05.382][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:05.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:05.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:05.386][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:05.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:05.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:05.390][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:05.391][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-21 23:38:05.391][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-21 23:38:05.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:05.394][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:05.395][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:05.396][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:05.398][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-21 23:38:05.401][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-21 23:38:05.407][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:38:05.408][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-21 23:38:05.410][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:38:05.412][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-21 23:38:05.414][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-21 23:38:05.416][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-21 23:38:05.418][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-21 23:38:05.419][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-21 23:38:05.421][biodb::testThat]
biodb.INFO [2024-05-21 23:38:05.422][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-05-21 23:38:05.424][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:38:05.425][biodb::testThat]
biodb.DEBUG[2024-05-21 23:38:05.432][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-05-21 23:38:05.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:05.444][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:38:05.447][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-05-21 23:38:05.740][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride does not exist.
biodb.TRACE[2024-05-21 23:38:05.742][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:05.745][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:05.748][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-05-21 23:38:06.335][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:38:06.339][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-05-21 23:38:06.347][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-05-21 23:38:06.373][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-05-21 23:38:06.377][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:06.378][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:06.380][rule$waitAsNeeded] Wait 0.065577 second(s).
biodb.TRACE[2024-05-21 23:38:06.459][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-05-21 23:38:06.743][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty does not exist.
biodb.TRACE[2024-05-21 23:38:06.744][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:06.746][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:06.748][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-05-21 23:38:07.336][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:38:07.340][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-05-21 23:38:07.349][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-05-21 23:38:07.374][biodb::testThat]
biodb.INFO [2024-05-21 23:38:07.376][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-05-21 23:38:07.379][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:38:07.381][biodb::testThat]
biodb.INFO [2024-05-21 23:38:07.428][biodb::testThat]
biodb.INFO [2024-05-21 23:38:07.430][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-05-21 23:38:07.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:38:07.435][biodb::testThat]
biodb.DEBUG[2024-05-21 23:38:07.440][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-21 23:38:07.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:07.448][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:07.450][rule$waitAsNeeded] Wait 0.008003 second(s).
biodb.TRACE[2024-05-21 23:38:07.476][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-05-21 23:38:07.763][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-05-21 23:38:07.765][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:07.767][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:07.768][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-05-21 23:38:08.180][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:38:08.183][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-05-21 23:38:08.188][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-05-21 23:38:08.195][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-21 23:38:08.199][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-21 23:38:08.200][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-21 23:38:08.202][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-21 23:38:08.208][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-21 23:38:08.215][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-05-21 23:38:08.219][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:08.220][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:08.221][rule$waitAsNeeded] Wait 0.252736 second(s).
biodb.TRACE[2024-05-21 23:38:08.477][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-05-21 23:38:08.759][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-05-21 23:38:08.761][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:08.763][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:08.765][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-05-21 23:38:09.174][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:38:09.192][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-05-21 23:38:09.198][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-05-21 23:38:09.207][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-05-21 23:38:09.213][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:09.214][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:09.216][rule$waitAsNeeded] Wait 0.260339 second(s).
biodb.TRACE[2024-05-21 23:38:09.482][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-05-21 23:38:09.768][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid does not exist.
biodb.TRACE[2024-05-21 23:38:09.770][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:09.771][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:09.773][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-05-21 23:38:11.315][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:38:11.318][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-05-21 23:38:11.337][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-05-21 23:38:11.540][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-05-21 23:38:11.547][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:11.549][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:38:11.551][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-05-21 23:38:11.845][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[2024-05-21 23:38:11.847][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:11.850][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[2024-05-21 23:38:11.853][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[2024-05-21 23:38:13.373][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-21 23:38:13.376][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-05-21 23:38:13.394][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-05-21 23:38:13.858][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-21 23:38:13.860][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-21 23:38:13.861][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-21 23:38:13.862][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-21 23:38:13.863][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:13.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:13.866][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:13.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:13.868][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-21 23:38:13.874][biodb::testContext]
biodb.INFO [2024-05-21 23:38:13.875][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-21 23:38:13.876][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-05-21 23:38:13.877][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-21 23:38:13.878][biodb::testContext]
biodb.INFO [2024-05-21 23:38:13.881][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-21 23:38:13.884][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-21 23:38:13.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:38:13.891][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-21 23:38:13.892][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-21 23:38:13.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.896][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-21 23:38:13.898][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-21 23:38:13.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.902][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-21 23:38:13.903][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-21 23:38:13.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.908][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-21 23:38:13.909][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-21 23:38:13.910][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-21 23:38:13.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.915][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-21 23:38:13.916][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-21 23:38:13.917][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-21 23:38:13.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.922][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-21 23:38:13.923][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-21 23:38:13.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.927][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[2024-05-21 23:38:13.928][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-21 23:38:13.929][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-21 23:38:13.930][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-21 23:38:13.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.935][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-21 23:38:13.936][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-21 23:38:13.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.941][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-21 23:38:13.942][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-21 23:38:13.943][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-21 23:38:13.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.947][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-21 23:38:13.949][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-21 23:38:13.950][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-21 23:38:13.951][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-21 23:38:13.952][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-21 23:38:13.954][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-21 23:38:13.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.958][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-21 23:38:13.960][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-21 23:38:13.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.964][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-21 23:38:13.966][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-21 23:38:13.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.970][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-21 23:38:13.971][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-21 23:38:13.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.976][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-21 23:38:13.977][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-21 23:38:13.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.980][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[2024-05-21 23:38:13.982][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-21 23:38:13.983][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-21 23:38:13.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.987][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-21 23:38:13.989][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-21 23:38:13.993][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-21 23:38:13.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:13.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:13.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:13.998][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-21 23:38:14.000][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-21 23:38:14.001][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-21 23:38:14.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.006][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-21 23:38:14.008][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.009][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-21 23:38:14.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:14.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.018][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:38:14.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:14.020][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.022][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-21 23:38:14.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:14.024][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.025][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.027][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:38:14.027][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:38:14.027][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-21 23:38:14.027][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-21 23:38:14.027][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-21 23:38:14.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:14.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.032][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:14.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.036][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.038][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:14.039][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:14.040][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.041][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.043][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-21 23:38:14.045][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.046][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-21 23:38:14.047][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.048][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:14.049][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.052][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.053][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.054][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-21 23:38:14.056][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:14.057][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.058][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-21 23:38:14.059][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:14.061][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.062][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.063][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:38:14.063][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:38:14.063][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-21 23:38:14.063][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-21 23:38:14.063][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-21 23:38:14.064][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:14.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.068][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:14.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.073][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.074][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.075][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:14.076][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:14.078][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.079][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.080][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-21 23:38:14.082][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.084][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-21 23:38:14.085][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.086][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:14.087][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.088][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.090][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.091][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.092][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:38:14.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:14.095][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.096][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-21 23:38:14.097][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:14.098][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.099][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.101][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.102][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:14.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:14.107][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.109][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.110][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.111][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:14.113][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:14.114][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.115][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.116][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-21 23:38:14.118][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.120][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-21 23:38:14.137][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:14.140][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.141][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.142][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.144][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.145][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-21 23:38:14.146][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:14.147][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.149][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-21 23:38:14.150][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:14.151][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.152][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.154][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.155][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:14.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.158][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:14.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.162][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.163][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.164][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:14.165][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:14.166][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.168][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.169][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:38:14.170][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.189][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[2024-05-21 23:38:14.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.200][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[2024-05-21 23:38:14.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.206][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[2024-05-21 23:38:14.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.217][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[2024-05-21 23:38:14.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.233][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[2024-05-21 23:38:14.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.263][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[2024-05-21 23:38:14.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.270][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-21 23:38:14.272][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-21 23:38:14.274][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-21 23:38:14.275][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-21 23:38:14.277][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-21 23:38:14.278][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-21 23:38:14.280][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-21 23:38:14.282][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-21 23:38:14.283][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-21 23:38:14.285][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-21 23:38:14.286][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-21 23:38:14.288][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-21 23:38:14.290][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-21 23:38:14.291][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-21 23:38:14.293][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-21 23:38:14.294][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-21 23:38:14.296][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-21 23:38:14.298][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-21 23:38:14.299][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-21 23:38:14.301][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-21 23:38:14.303][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-21 23:38:14.304][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-21 23:38:14.306][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-21 23:38:14.307][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-21 23:38:14.309][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-21 23:38:14.311][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-21 23:38:14.312][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-21 23:38:14.314][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-21 23:38:14.315][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-21 23:38:14.317][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-21 23:38:14.318][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-21 23:38:14.320][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-21 23:38:14.322][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-21 23:38:14.323][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-21 23:38:14.325][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-21 23:38:14.326][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-21 23:38:14.328][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-21 23:38:14.329][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-21 23:38:14.331][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-21 23:38:14.333][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-21 23:38:14.334][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-21 23:38:14.336][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-21 23:38:14.337][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-21 23:38:14.339][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-21 23:38:14.341][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-21 23:38:14.342][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-21 23:38:14.344][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-21 23:38:14.345][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-21 23:38:14.347][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-21 23:38:14.349][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-21 23:38:14.350][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-21 23:38:14.352][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-21 23:38:14.353][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-21 23:38:14.355][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-21 23:38:14.356][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-21 23:38:14.358][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-21 23:38:14.360][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-21 23:38:14.361][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-21 23:38:14.363][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-21 23:38:14.364][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-21 23:38:14.366][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-21 23:38:14.367][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-21 23:38:14.369][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-21 23:38:14.371][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-21 23:38:14.372][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-21 23:38:14.374][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-21 23:38:14.375][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-21 23:38:14.377][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-21 23:38:14.379][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-21 23:38:14.380][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-21 23:38:14.382][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-21 23:38:14.383][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-21 23:38:14.385][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-21 23:38:14.386][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-21 23:38:14.388][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-21 23:38:14.390][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-21 23:38:14.391][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-21 23:38:14.393][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-21 23:38:14.394][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-21 23:38:14.396][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-21 23:38:14.397][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-21 23:38:14.399][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-21 23:38:14.401][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-21 23:38:14.402][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-21 23:38:14.405][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-21 23:38:14.406][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-21 23:38:14.407][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.409][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.495][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[2024-05-21 23:38:14.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.506][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[2024-05-21 23:38:14.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.531][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[2024-05-21 23:38:14.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.556][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[2024-05-21 23:38:14.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-21 23:38:14.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:14.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:14.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:14.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:14.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:14.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:14.610][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-21 23:38:14.613][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:38:14.616][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.619][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.621][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.623][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-21 23:38:14.624][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.626][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.627][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.628][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.629][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-21 23:38:14.631][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-21 23:38:14.632][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.633][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-21 23:38:14.635][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-21 23:38:14.636][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-21 23:38:14.637][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-21 23:38:14.638][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-21 23:38:14.638][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-21 23:38:14.640][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-21 23:38:14.641][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.642][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.643][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-21 23:38:14.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-21 23:38:14.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-21 23:38:14.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-21 23:38:14.648][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-21 23:38:14.648][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-21 23:38:14.650][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-21 23:38:14.651][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-21 23:38:14.652][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-21 23:38:14.653][self$setPropertyValue]
biodb.DEBUG[2024-05-21 23:38:14.655][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-21 23:38:14.657][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-21 23:38:14.660][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:38:14.661][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-21 23:38:14.663][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-21 23:38:14.665][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-21 23:38:14.668][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-21 23:38:14.669][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-21 23:38:14.671][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-21 23:38:14.672][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-21 23:38:14.675][biodb::testThat]
biodb.INFO [2024-05-21 23:38:14.676][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-05-21 23:38:14.677][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-21 23:38:14.678][biodb::testThat]
biodb.DEBUG[2024-05-21 23:38:14.683][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-21 23:38:14.689][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-21 23:38:14.691][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-21 23:38:14.692][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-21 23:38:14.816][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-05-21 23:38:16.353][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-05-21 23:38:16.355][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-21 23:38:16.357][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-05-21 23:38:16.359][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-21 23:38:16.360][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-21 23:38:16.362][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-21 23:38:16.363][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-21 23:38:16.364][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-21 23:38:16.365][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-21 23:38:16.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:38:16.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:16.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:16.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:16.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:16.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:16.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:16.384][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-05-21 23:38:16.387][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:16.388][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-21 23:38:16.390][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:16.674][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:16.675][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:16.677][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[2024-05-21 23:38:16.679][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:17.270][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:17.273][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:17.275][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:17.277][rule$waitAsNeeded] Wait 0.112977 second(s).
biodb.TRACE[2024-05-21 23:38:17.394][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:17.688][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:17.690][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:17.692][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:17.693][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:18.290][private$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[2024-05-21 23:38:18.292][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:18.294][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:18.296][rule$waitAsNeeded] Wait 0.097923 second(s).
biodb.TRACE[2024-05-21 23:38:18.398][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:18.684][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:18.685][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:18.687][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[2024-05-21 23:38:18.688][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:19.275][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:19.277][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:19.279][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:19.281][rule$waitAsNeeded] Wait 0.115891 second(s).
biodb.TRACE[2024-05-21 23:38:19.413][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:19.696][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:19.698][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:19.699][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:19.701][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:20.290][private$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[2024-05-21 23:38:20.292][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:20.293][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:20.294][rule$waitAsNeeded] Wait 0.118427 second(s).
biodb.TRACE[2024-05-21 23:38:20.429][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:20.713][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:20.716][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:20.717][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[2024-05-21 23:38:20.718][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:21.306][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:21.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:21.311][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:21.313][rule$waitAsNeeded] Wait 0.115926 second(s).
biodb.TRACE[2024-05-21 23:38:21.446][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:21.734][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:21.736][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:21.737][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:21.739][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:22.326][private$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[2024-05-21 23:38:22.327][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:22.329][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:22.330][rule$waitAsNeeded] Wait 0.114728 second(s).
biodb.TRACE[2024-05-21 23:38:22.449][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:22.736][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:22.738][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:22.739][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[2024-05-21 23:38:22.740][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:23.330][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:23.332][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:23.335][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:23.337][rule$waitAsNeeded] Wait 0.112236 second(s).
biodb.TRACE[2024-05-21 23:38:23.453][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:23.736][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:23.738][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:23.739][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:23.741][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:24.332][private$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[2024-05-21 23:38:24.334][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:24.335][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:24.337][rule$waitAsNeeded] Wait 0.115989 second(s).
biodb.TRACE[2024-05-21 23:38:24.457][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:24.741][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:24.742][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:24.743][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[2024-05-21 23:38:24.745][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:25.338][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:25.341][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:25.343][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:25.345][rule$waitAsNeeded] Wait 0.112016 second(s).
biodb.TRACE[2024-05-21 23:38:25.461][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-21 23:38:25.750][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:25.751][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:25.753][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:25.754][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-21 23:38:26.337][private$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[2024-05-21 23:38:26.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:38:26.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:26.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:26.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:26.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:26.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:26.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-21 23:38:26.384][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-05-21 23:38:26.388][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:26.389][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:26.392][rule$waitAsNeeded] Wait 0.0688791 second(s).
biodb.TRACE[2024-05-21 23:38:26.477][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:26.763][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:26.765][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:26.766][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:26.768][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:27.354][private$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[2024-05-21 23:38:27.357][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:27.359][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:27.361][rule$waitAsNeeded] Wait 0.115501 second(s).
biodb.TRACE[2024-05-21 23:38:27.493][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:27.779][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:27.780][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:27.782][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[2024-05-21 23:38:27.783][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:28.369][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:28.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:28.372][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:28.374][rule$waitAsNeeded] Wait 0.118505 second(s).
biodb.TRACE[2024-05-21 23:38:28.509][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:28.803][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:28.805][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:28.806][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:28.808][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:29.402][private$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[2024-05-21 23:38:29.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:29.407][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:29.409][rule$waitAsNeeded] Wait 0.0997241 second(s).
biodb.TRACE[2024-05-21 23:38:29.525][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:29.812][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:29.813][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:29.815][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[2024-05-21 23:38:29.816][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:30.403][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:30.406][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:30.408][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:30.410][rule$waitAsNeeded] Wait 0.114696 second(s).
biodb.TRACE[2024-05-21 23:38:30.542][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:30.833][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:30.835][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:30.838][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:30.840][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:31.435][private$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[2024-05-21 23:38:31.438][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:31.440][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:31.443][rule$waitAsNeeded] Wait 0.099169 second(s).
biodb.TRACE[2024-05-21 23:38:31.559][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:31.855][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:31.857][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:31.860][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[2024-05-21 23:38:31.862][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:32.451][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:32.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:32.456][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:32.458][rule$waitAsNeeded] Wait 0.09952 second(s).
biodb.TRACE[2024-05-21 23:38:32.575][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:32.869][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:32.871][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:32.873][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:32.876][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:33.467][private$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[2024-05-21 23:38:33.469][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:33.470][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:33.472][rule$waitAsNeeded] Wait 0.10192 second(s).
biodb.TRACE[2024-05-21 23:38:33.591][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:33.885][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:33.886][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:33.887][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[2024-05-21 23:38:33.889][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:34.475][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-21 23:38:34.477][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:34.480][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:34.482][rule$waitAsNeeded] Wait 0.108044 second(s).
biodb.TRACE[2024-05-21 23:38:34.598][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:34.888][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:34.889][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:34.891][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-21 23:38:34.892][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:35.475][private$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[2024-05-21 23:38:35.478][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-21 23:38:35.480][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-21 23:38:35.482][rule$waitAsNeeded] Wait 0.115492 second(s).
biodb.TRACE[2024-05-21 23:38:35.614][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-21 23:38:35.907][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-21 23:38:35.909][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-21 23:38:35.912][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[2024-05-21 23:38:35.914][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-21 23:38:36.506][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-21 23:38:36.510][private$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[2024-05-21 23:38:36.513][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-21 23:38:36.515][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-21 23:38:36.517][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-21 23:38:36.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:38:36.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:36.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:36.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:36.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:36.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:36.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:38:36.546][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:38:36.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:38:36.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.551][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:38:36.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:38:36.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:38:36.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:38:36.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:36.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:36.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:36.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:36.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:36.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:38:36.649][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:38:36.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:38:36.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.655][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:38:36.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-21 23:38:36.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-21 23:38:36.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-21 23:38:36.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-21 23:38:36.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-21 23:38:36.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-21 23:38:36.721][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-21 23:38:36.722][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-21 23:38:36.725][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-21 23:38:36.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:38:36.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:36.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:36.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:36.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:36.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:36.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:38:36.752][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-05-21 23:38:36.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-21 23:38:36.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:36.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:36.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:36.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:36.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:36.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-21 23:38:36.768][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-05-21 23:38:36.770][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-05-21 23:38:36.771][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-05-21 23:38:36.793][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-21 23:38:36.796][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-21 23:38:36.798][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-21 23:38:36.799][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-21 23:38:36.801][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-21 23:38:36.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-21 23:38:36.804][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-21 23:38:36.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-21 23:38:36.808][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-21 23:38:36.809][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".
[ 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 3.79 1.8856.39
LipidmapsStructureEntry0.650.000.66