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This page was generated on 2023-05-26 06:18:05 -0000 (Fri, 26 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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CHECK results for biodbLipidmaps on kunpeng2


To the developers/maintainers of the biodbLipidmaps package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 195/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.7.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: devel
git_last_commit: 0466597
git_last_commit_date: 2023-04-25 15:34:40 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

Summary

Package: biodbLipidmaps
Version: 1.7.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biodbLipidmaps_1.7.0.tar.gz
StartedAt: 2023-05-26 04:07:43 -0000 (Fri, 26 May 2023)
EndedAt: 2023-05-26 04:13:24 -0000 (Fri, 26 May 2023)
EllapsedTime: 341.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biodbLipidmaps_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
          name = request.key, ext = "request")
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─conn$annotateMzValues(...)
   4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
   5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
   6.         └─self$wsLmsdSearch(...)
   7.           └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘biodbLipidmaps.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2023-05-26 04:08:50.745][biodb::testContext]
biodb.INFO [2023-05-26 04:08:50.747][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:08:50.749][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-05-26 04:08:50.750][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:08:50.751][biodb::testContext]
biodb.INFO [2023-05-26 04:08:50.771][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:08:50.774][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-26 04:08:50.783][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:08:50.784][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-26 04:08:50.786][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-26 04:08:50.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.791][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-26 04:08:50.819][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-26 04:08:50.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.824][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-26 04:08:50.826][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-26 04:08:50.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.831][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-26 04:08:50.832][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-26 04:08:50.833][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-26 04:08:50.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.838][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-26 04:08:50.840][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-26 04:08:50.841][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-26 04:08:50.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.846][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-26 04:08:50.848][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-26 04:08:50.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.853][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-26 04:08:50.854][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-26 04:08:50.855][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-26 04:08:50.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.860][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-26 04:08:50.862][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-26 04:08:50.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.867][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-26 04:08:50.868][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-26 04:08:50.870][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-26 04:08:50.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.875][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:08:50.876][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-26 04:08:50.877][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-26 04:08:50.879][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-26 04:08:50.880][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-26 04:08:50.882][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-26 04:08:50.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.887][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-26 04:08:50.888][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-26 04:08:50.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.893][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-26 04:08:50.895][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-26 04:08:50.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.899][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[2023-05-26 04:08:50.900][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-26 04:08:50.901][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-26 04:08:50.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.906][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-26 04:08:50.908][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-26 04:08:50.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.913][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-26 04:08:50.914][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-26 04:08:50.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.919][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:08:50.921][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-26 04:08:50.926][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-26 04:08:50.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.931][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-26 04:08:50.932][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-26 04:08:50.934][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-26 04:08:50.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:50.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:50.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:50.942][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-26 04:08:50.991][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.027][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-26 04:08:51.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:51.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.034][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.035][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.036][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:08:51.038][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:51.039][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.040][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-26 04:08:51.041][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:51.043][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.044][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.045][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:08:51.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:08:51.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:08:51.045][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:08:51.045][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:08:51.047][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:51.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.050][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:51.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.054][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.055][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.057][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:51.058][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:51.059][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.060][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.062][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-26 04:08:51.064][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.066][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:08:51.067][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.069][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:51.070][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.071][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.073][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.075][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:08:51.077][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:51.078][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.080][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-26 04:08:51.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:51.082][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.084][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.085][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:08:51.085][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:08:51.085][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:08:51.085][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:08:51.085][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:08:51.086][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:51.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.090][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:51.092][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.094][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.095][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.097][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:51.098][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:51.099][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.101][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.102][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-26 04:08:51.105][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.106][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-26 04:08:51.107][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:51.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.113][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.116][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:08:51.117][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:51.118][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.120][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-26 04:08:51.121][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:51.122][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.124][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.125][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.126][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:51.128][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.129][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.130][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:51.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.134][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.135][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.137][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:51.138][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:51.139][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.140][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.142][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-26 04:08:51.144][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.146][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:08:51.147][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.148][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:51.150][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.151][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.152][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.154][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.155][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:08:51.156][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:51.158][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.159][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-26 04:08:51.160][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:51.161][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.163][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.164][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:51.167][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.168][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.169][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:51.171][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.172][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.173][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.174][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.176][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:51.177][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:51.178][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.179][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.184][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:08:51.186][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.228][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[2023-05-26 04:08:51.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.269][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[2023-05-26 04:08:51.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.289][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-26 04:08:51.295][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-26 04:08:51.297][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-26 04:08:51.299][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-26 04:08:51.301][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:08:51.303][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-26 04:08:51.305][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-26 04:08:51.306][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-26 04:08:51.308][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-26 04:08:51.310][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-26 04:08:51.312][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:08:51.314][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-26 04:08:51.316][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-26 04:08:51.318][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-26 04:08:51.320][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-26 04:08:51.322][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:08:51.324][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-26 04:08:51.326][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-26 04:08:51.328][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:08:51.330][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-26 04:08:51.332][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-26 04:08:51.334][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-26 04:08:51.336][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-26 04:08:51.338][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-26 04:08:51.340][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-26 04:08:51.342][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-26 04:08:51.344][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-26 04:08:51.346][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-26 04:08:51.347][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-26 04:08:51.349][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-26 04:08:51.351][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-26 04:08:51.361][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-26 04:08:51.363][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-26 04:08:51.365][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-26 04:08:51.367][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-26 04:08:51.369][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-26 04:08:51.371][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-26 04:08:51.373][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-26 04:08:51.375][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-26 04:08:51.377][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-26 04:08:51.379][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-26 04:08:51.380][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-26 04:08:51.382][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-26 04:08:51.384][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-26 04:08:51.386][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-26 04:08:51.388][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-26 04:08:51.390][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-26 04:08:51.392][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-26 04:08:51.394][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-26 04:08:51.396][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-26 04:08:51.398][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-26 04:08:51.400][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-26 04:08:51.401][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-26 04:08:51.403][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-26 04:08:51.405][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-26 04:08:51.407][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-26 04:08:51.409][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-26 04:08:51.411][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-26 04:08:51.413][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-26 04:08:51.415][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-26 04:08:51.417][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-26 04:08:51.419][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-26 04:08:51.421][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-26 04:08:51.423][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-26 04:08:51.425][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-26 04:08:51.427][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-26 04:08:51.429][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:08:51.431][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:08:51.433][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-26 04:08:51.435][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-26 04:08:51.437][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-26 04:08:51.439][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-26 04:08:51.441][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-26 04:08:51.443][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-26 04:08:51.445][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-26 04:08:51.447][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-26 04:08:51.449][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-26 04:08:51.451][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-26 04:08:51.453][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-26 04:08:51.455][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-26 04:08:51.457][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-26 04:08:51.459][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-26 04:08:51.461][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-26 04:08:51.469][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-26 04:08:51.471][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:08:51.475][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:08:51.477][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.479][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.480][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[2023-05-26 04:08:51.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.544][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[2023-05-26 04:08:51.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.569][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[2023-05-26 04:08:51.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.602][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[2023-05-26 04:08:51.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.618][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[2023-05-26 04:08:51.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:51.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:51.629][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-26 04:08:51.643][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:08:51.645][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.647][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.648][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.650][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:51.651][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.653][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.654][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.655][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.657][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:08:51.658][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:51.660][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.661][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-26 04:08:51.663][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-26 04:08:51.664][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-26 04:08:51.666][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:51.667][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:08:51.667][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:08:51.668][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:51.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.673][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:51.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:51.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:51.676][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:51.678][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-26 04:08:51.678][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-26 04:08:51.679][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:51.680][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:51.682][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:51.683][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:51.692][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-26 04:08:51.702][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:08:51.732][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:08:51.734][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-26 04:08:51.739][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:08:51.744][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-26 04:08:51.749][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-26 04:08:51.751][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-26 04:08:51.752][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-26 04:08:51.754][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-26 04:08:51.774][biodb::testThat]
biodb.INFO [2023-05-26 04:08:51.776][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-05-26 04:08:51.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:51.778][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:51.783][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-05-26 04:08:51.789][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:51.794][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-26 04:08:51.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:51.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:51.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:51.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:51.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:51.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:51.828][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[2023-05-26 04:08:51.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:51.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:51.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:51.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:51.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:51.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:51.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.880][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:08:51.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:08:51.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.885][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:51.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:51.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:51.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:51.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.931][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:51.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:51.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:51.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:51.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.946][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:51.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:51.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.955][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:08:51.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:51.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.961][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:08:51.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:51.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.970][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:51.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:51.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.975][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:51.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:51.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:51.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:51.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:51.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:51.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:51.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:51.999][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:08:52.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.004][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-26 04:08:52.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.021][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:08:52.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.147][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.152][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.162][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:52.203][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-05-26 04:08:52.210][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:52.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:52.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.216][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:52.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:52.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.221][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:52.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:52.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.226][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:52.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:52.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.273][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.320][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.326][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.331][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.372][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.374][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.375][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.376][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.409][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.411][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.412][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.413][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.430][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.436][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.446][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.448][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.449][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.450][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.452][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:52.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:52.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.472][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:52.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:52.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.477][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:52.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:52.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.483][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:52.484][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:52.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.487][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:52.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:52.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.519][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.520][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.523][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.540][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.546][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.551][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.557][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.559][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.560][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.561][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.563][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.578][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.580][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.582][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.590][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.592][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.594][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.602][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:52.604][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:52.605][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.606][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.614][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.615][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.617][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.618][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.625][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.627][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.628][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.629][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.637][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.639][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.641][ef$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:52.650][biodb::testThat]
biodb.INFO [2023-05-26 04:08:52.651][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-05-26 04:08:52.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:52.654][biodb::testThat]
biodb.DEBUG[2023-05-26 04:08:52.710][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-05-26 04:08:52.719][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:08:52.723][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-05-26 04:08:52.725][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:52.727][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-05-26 04:08:52.728][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:08:52.790][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:52.792][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-26 04:08:52.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:52.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:52.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:52.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:52.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:52.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:52.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:52.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:52.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:52.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:52.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:52.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:52.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:52.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.843][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:08:52.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:08:52.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.849][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:52.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:52.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.854][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.860][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:08:52.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.869][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:08:52.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.883][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:08:52.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.888][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:08:52.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:52.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:52.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:52.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:52.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:52.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.926][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:08:52.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.932][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-26 04:08:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.937][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.948][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:08:52.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:52.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:52.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:52.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:52.988][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:52.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:53.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.003][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:53.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:53.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:53.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:53.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.013][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:53.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:08:53.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:53.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:53.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:53.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:53.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:53.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:53.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:53.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:53.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:53.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:53.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:53.055][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-05-26 04:08:53.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-05-26 04:08:53.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-05-26 04:08:53.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-05-26 04:08:53.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-05-26 04:08:53.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-05-26 04:08:53.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-05-26 04:08:53.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:53.080][biodb::testThat]
biodb.INFO [2023-05-26 04:08:53.081][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-05-26 04:08:53.083][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:53.084][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:53.087][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:53.089][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:53.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.091][ef$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:53.093][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-05-26 04:08:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:53.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:53.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:53.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:53.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:53.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:53.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:53.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:53.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:53.149][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-26 04:08:53.166][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-26 04:08:53.195][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:53.196][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:53.198][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-05-26 04:08:54.324][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-05-26 04:08:55.279][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:55.294][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-05-26 04:08:55.339][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-05-26 04:08:55.348][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-05-26 04:08:55.378][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:55.380][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:55.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.384][ef$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:55.388][biodb::testThat]
biodb.INFO [2023-05-26 04:08:55.390][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-05-26 04:08:55.392][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:55.394][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:55.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:55.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:55.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:55.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:55.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:55.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:55.684][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-26 04:08:55.689][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:08:55.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-26 04:08:55.715][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:55.717][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-05-26 04:08:55.750][biodb::testThat]
biodb.INFO [2023-05-26 04:08:55.751][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-05-26 04:08:55.753][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:55.754][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:55.793][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:55.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:55.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.799][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:55.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:55.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.805][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:55.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:55.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:55.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:55.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.883][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:55.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:55.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.889][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:55.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:55.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.895][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:55.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:55.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.901][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:55.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:55.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:55.910][biodb::testThat]
biodb.INFO [2023-05-26 04:08:55.912][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-05-26 04:08:55.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:55.915][biodb::testThat]
biodb.INFO [2023-05-26 04:08:55.922][biodb::testThat]
biodb.INFO [2023-05-26 04:08:55.924][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-05-26 04:08:55.925][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:55.926][biodb::testThat]
biodb.INFO [2023-05-26 04:08:55.933][biodb::testThat]
biodb.INFO [2023-05-26 04:08:55.934][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-05-26 04:08:55.936][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:55.937][biodb::testThat]
biodb.DEBUG[2023-05-26 04:08:55.942][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-05-26 04:08:57.792][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-05-26 04:08:58.478][biodb::testThat]
biodb.INFO [2023-05-26 04:08:58.479][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-05-26 04:08:58.480][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:58.481][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:58.504][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:58.505][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:58.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.508][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.509][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.511][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.513][ef$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:58.516][biodb::testThat]
biodb.INFO [2023-05-26 04:08:58.517][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-05-26 04:08:58.518][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:58.519][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:58.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:58.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:58.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:58.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:58.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:58.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:58.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:58.672][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-26 04:08:58.676][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:08:58.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-26 04:08:58.680][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:58.682][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-05-26 04:08:58.795][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-26 04:08:58.799][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:08:58.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-26 04:08:58.802][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:58.804][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-05-26 04:08:58.826][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-26 04:08:58.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-26 04:08:58.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:58.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:58.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:58.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:58.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:58.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:58.938][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-05-26 04:08:58.961][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:58.962][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:58.993][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-05-26 04:09:03.078][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-05-26 04:09:18.193][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:18.203][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-05-26 04:09:18.244][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-05-26 04:09:19.472][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[2023-05-26 04:09:19.477][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:19.479][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:19.481][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-05-26 04:09:20.430][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-05-26 04:09:21.378][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:21.388][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-05-26 04:09:21.404][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-05-26 04:09:21.501][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-05-26 04:09:21.505][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:21.507][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:21.510][private$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[2023-05-26 04:09:22.421][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2023-05-26 04:09:23.407][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:23.415][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-05-26 04:09:23.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-05-26 04:09:23.460][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-26 04:09:23.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-26 04:09:23.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:23.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:09:23.480][biodb::testThat]
biodb.INFO [2023-05-26 04:09:23.482][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-05-26 04:09:23.483][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:09:23.484][biodb::testThat]
biodb.TRACE[2023-05-26 04:09:23.488][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-26 04:09:23.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-26 04:09:23.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:23.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:23.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:23.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:23.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:23.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:23.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:23.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:23.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:23.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:23.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:23.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:23.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:23.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:23.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:23.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:23.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:23.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:23.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:23.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:23.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:23.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:23.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:23.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:23.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:23.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:23.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:23.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:23.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:23.618][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-05-26 04:09:23.622][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:23.624][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:23.626][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-05-26 04:09:28.286][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-05-26 04:09:58.693][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:58.703][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-05-26 04:09:58.745][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-05-26 04:09:59.859][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-05-26 04:09:59.925][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-26 04:09:59.927][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-05-26 04:09:59.929][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-05-26 04:09:59.930][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:59.932][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:59.933][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-26 04:09:59.935][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:59.936][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:59.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:59.973][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-05-26 04:09:59.977][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:59.978][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:59.980][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-05-26 04:10:00.878][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-05-26 04:10:01.847][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:01.857][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-05-26 04:10:01.872][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-05-26 04:10:01.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:01.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:01.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:01.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:01.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:01.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:01.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:01.895][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-05-26 04:10:01.898][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:01.900][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:01.902][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-05-26 04:10:02.850][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-05-26 04:10:04.265][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:04.276][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-05-26 04:10:04.290][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-05-26 04:10:04.303][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2023-05-26 04:10:04.308][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:10:04.333][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-26 04:10:04.335][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-26 04:10:04.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:04.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:04.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:04.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:04.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:04.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:04.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:04.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:04.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:04.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:04.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:04.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.408][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:10:04.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:10:04.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.414][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:04.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:04.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.419][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:10:04.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:10:04.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:10:04.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:10:04.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.434][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:10:04.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:10:04.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:10:04.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:10:04.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.449][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:10:04.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:04.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.455][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:10:04.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:04.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.464][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:04.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:04.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:04.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:04.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:04.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:04.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.495][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:10:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.500][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-26 04:10:04.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:04.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:04.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.517][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:10:04.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.526][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.532][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.543][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:04.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:04.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:04.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:04.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:04.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:04.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:04.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:04.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:04.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:04.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:10:04.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:10:04.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:04.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:04.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.640][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:10:04.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:10:04.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:10:04.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:10:04.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.654][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:10:04.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:10:04.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:10:04.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:10:04.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.669][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:10:04.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:04.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.675][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:10:04.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:04.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.685][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:04.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:04.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.690][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:04.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:04.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:04.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:04.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:10:04.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.721][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-26 04:10:04.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:04.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:04.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.737][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:10:04.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.746][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.752][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.763][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:04.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:04.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:04.839][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-05-26 04:10:04.852][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:10:04.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:04.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:04.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:04.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:04.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:04.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:04.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:04.870][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.875][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.881][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:04.882][private$selectFields]
biodb.TRACE[2023-05-26 04:10:04.884][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:04.885][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:04.886][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:04.888][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.889][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.892][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.893][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.894][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.896][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.897][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.898][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:04.900][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:04.901][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.902][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.904][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.905][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.906][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-26 04:10:04.908][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.913][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.918][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.936][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-05-26 04:10:04.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:04.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:04.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:04.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:04.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:04.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:04.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:04.954][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.959][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.965][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:04.966][private$selectFields]
biodb.TRACE[2023-05-26 04:10:04.967][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:04.968][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:04.970][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:04.971][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.973][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.974][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.975][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.976][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.978][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.979][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.980][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.982][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:04.983][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:04.985][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.986][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.989][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.990][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-26 04:10:04.991][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:04.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:04.997][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:04.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.020][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.026][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-05-26 04:10:05.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:05.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:05.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:05.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:05.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:05.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:05.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:05.043][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.048][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.053][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:05.055][private$selectFields]
biodb.TRACE[2023-05-26 04:10:05.056][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:05.057][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:05.059][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:05.060][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.061][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.063][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.064][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.065][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.067][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.069][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.071][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:05.072][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:10:05.073][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.075][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.077][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.079][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-26 04:10:05.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.086][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.091][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:10:05.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.097][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-05-26 04:10:05.098][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:10:05.100][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-26 04:10:05.113][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-26 04:10:05.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-26 04:10:05.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:10:05.119][biodb::testThat]
biodb.INFO [2023-05-26 04:10:05.121][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-05-26 04:10:05.122][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:05.123][biodb::testThat]
biodb.TRACE[2023-05-26 04:10:05.127][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-26 04:10:05.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-26 04:10:05.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:05.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:05.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:05.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:05.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:05.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:05.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:05.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:05.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:05.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:05.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:05.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:05.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:05.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:05.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:05.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:05.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:05.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:05.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:05.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:05.345][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2023-05-26 04:10:05.349][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:05.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:05.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-05-26 04:10:09.927][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.INFO [2023-05-26 04:11:09.984][biodb::testThat]
biodb.INFO [2023-05-26 04:11:09.985][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-05-26 04:11:10.006][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:11:10.008][biodb::testThat]
biodb.TRACE[2023-05-26 04:11:10.012][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-26 04:11:10.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-26 04:11:10.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:10.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:10.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:11:10.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:11:10.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:10.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:10.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:10.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:10.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:10.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:10.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:10.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:10.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:10.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:10.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:10.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:10.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:10.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:10.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:10.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:10.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:10.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:11:10.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:10.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:10.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:10.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:10.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:10.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:10.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:11:10.123][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-05-26 04:11:10.128][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:11:10.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-05-26 04:11:10.131][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:11:10.221][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-05-26 04:11:11.711][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:11:11.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:11.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:11.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:11.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:11.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:11.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:11.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:11:11.779][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.785][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.820][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.822][private$selectFields]
biodb.TRACE[2023-05-26 04:11:11.823][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:11:11.824][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:11:11.826][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.827][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.828][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.830][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.831][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.833][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.834][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.836][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.837][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.838][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.853][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.855][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.857][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.861][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.862][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-26 04:11:11.864][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.869][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.875][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.880][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-05-26 04:11:11.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:11.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:11.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:11.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:11.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:11.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:11.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:11:11.898][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.904][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.909][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.911][private$selectFields]
biodb.TRACE[2023-05-26 04:11:11.912][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:11:11.913][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:11:11.915][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.916][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.918][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.919][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.920][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.922][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.923][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.924][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.925][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.927][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.928][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.929][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.931][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.932][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.933][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.934][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-26 04:11:11.936][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.946][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.952][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-05-26 04:11:11.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:11.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:11.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:11.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:11.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:11.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:11.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:11:11.971][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.977][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.983][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.984][private$selectFields]
biodb.TRACE[2023-05-26 04:11:11.986][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:11:11.987][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:11:11.989][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:11.990][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.992][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.993][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:11.995][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:11.996][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:11.998][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:12.001][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:12.003][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:12.004][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:11:12.006][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.007][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.009][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:12.011][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:12.012][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-26 04:11:12.014][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:12.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:12.021][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:12.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:12.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:12.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:12.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:12.034][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-05-26 04:11:12.036][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:11:12.038][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-26 04:11:12.071][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-26 04:11:12.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-26 04:11:12.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:12.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:11:12.112][biodb::testThat]
biodb.INFO [2023-05-26 04:11:12.113][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-05-26 04:11:12.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:11:12.116][biodb::testThat]
biodb.DEBUG[2023-05-26 04:11:12.118][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-05-26 04:11:12.120][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:11:12.122][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-05-26 04:11:12.124][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:11:12.125][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:11:12.127][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:11:12.128][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-26 04:11:12.129][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:11:12.131][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:11:12.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:12.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:12.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:12.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:12.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:12.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:12.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:11:12.166][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-05-26 04:11:12.170][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:12.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:12.173][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:13.209][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:13.210][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:13.212][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:13.213][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:14.244][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:14.246][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:14.247][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:14.249][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:15.147][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:15.149][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:15.150][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:15.152][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:16.183][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:16.184][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:16.185][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:16.187][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:17.068][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:17.069][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:17.071][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:17.072][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:18.104][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:18.107][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:18.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:18.110][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:19.024][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:19.025][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:19.027][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:19.028][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:20.059][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:20.061][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:20.062][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:20.064][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:21.395][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:21.397][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:21.398][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:21.400][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:22.430][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:22.431][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:22.433][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:22.434][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:23.314][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:23.315][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:23.317][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:23.318][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:24.348][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:24.349][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:24.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:24.352][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:25.256][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:25.257][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:25.259][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:25.260][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:26.290][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:26.291][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:26.293][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:26.294][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:27.174][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:27.176][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:27.177][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:27.178][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:28.244][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:28.245][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:28.247][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:28.249][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:29.141][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:29.143][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:29.144][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:29.145][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:30.177][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:30.179][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:30.180][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:30.182][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-26 04:11:31.090][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:31.092][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:31.093][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:31.095][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-26 04:11:32.128][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2023-05-26 04:11:32.138][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-05-26 04:11:32.144][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:11:32.166][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:11:32.168][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-26 04:11:32.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:32.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:32.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:32.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:32.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:32.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:32.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:11:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:32.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:32.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:32.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:32.193][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:32.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:32.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:32.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:32.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:32.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:32.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:32.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:32.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:32.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:32.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:32.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:32.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:32.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:32.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:32.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:32.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:32.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:32.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:32.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:32.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:32.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:32.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:32.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:32.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:32.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:11:32.233][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-05-26 04:11:32.234][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-05-26 04:11:32.243][biodb::testThat]
biodb.INFO [2023-05-26 04:11:32.245][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-05-26 04:11:32.246][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:11:32.248][biodb::testThat]
biodb.DEBUG[2023-05-26 04:11:32.259][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-05-26 04:11:32.261][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-05-26 04:11:32.262][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-26 04:11:32.264][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-05-26 04:11:32.266][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-05-26 04:11:32.268][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:11:32.269][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:11:32.271][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-26 04:11:32.272][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:11:32.273][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:11:32.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:32.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:32.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:32.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:32.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:32.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:32.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:11:32.295][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-05-26 04:11:32.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:32.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:32.302][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:33.211][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:33.212][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:33.214][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:33.215][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:34.246][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:34.247][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:34.249][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:34.250][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:35.165][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:35.166][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:35.168][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:35.169][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:36.201][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:36.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:36.204][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:36.206][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:37.109][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:37.110][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:37.112][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:37.113][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:38.143][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:38.144][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:38.146][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:38.147][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:39.081][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:39.082][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:39.084][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:39.085][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:40.116][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:40.117][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:40.119][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:40.120][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:40.986][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:40.987][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:40.989][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:40.990][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:42.022][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:42.023][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:42.024][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:42.026][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:44.414][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:44.416][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:44.417][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:44.418][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:45.449][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:45.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:45.452][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:45.454][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:48.308][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:48.309][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:48.310][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:48.312][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:49.342][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:49.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:49.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:49.347][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:50.256][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:50.257][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:50.259][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:50.260][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:51.291][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:51.292][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:51.293][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:51.295][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:52.206][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:52.208][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:52.209][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:52.210][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:53.240][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:53.242][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:53.243][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:53.245][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-26 04:11:54.140][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-26 04:11:54.144][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-26 04:11:54.146][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-26 04:11:54.148][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-26 04:11:55.392][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-26 04:11:55.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:55.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:55.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:55.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:55.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:55.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:55.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:11:55.419][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-05-26 04:11:55.424][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:55.426][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:55.428][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-05-26 04:11:56.380][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-05-26 04:11:57.343][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:11:57.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-05-26 04:11:57.369][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-05-26 04:11:57.474][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-05-26 04:11:57.481][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:11:57.514][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-26 04:11:57.516][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-26 04:11:57.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:57.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:57.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:57.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:57.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:57.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:57.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:11:57.540][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.548][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:11:57.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:11:57.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:11:57.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:11:57.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:11:57.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:11:57.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:11:57.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:11:57.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:11:57.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:11:57.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:11:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:11:57.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.631][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:11:57.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:11:57.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.638][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:11:57.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:11:57.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.650][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:11:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:11:57.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.657][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:11:57.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:11:57.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.669][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:11:57.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:11:57.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.677][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:11:57.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:11:57.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.689][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:11:57.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:11:57.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.697][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:11:57.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:11:57.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.710][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:11:57.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:57.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.718][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:11:57.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:11:57.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:11:57.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:11:57.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:11:57.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:11:57.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.766][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:11:57.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.772][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-26 04:11:57.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.790][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:11:57.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:11:57.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:11:57.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.835][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.841][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.852][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:11:57.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:11:57.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:11:57.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:11:57.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:11:57.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:11:57.926][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-05-26 04:11:57.927][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-05-26 04:11:57.929][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-05-26 04:11:57.946][biodb::testThat]
biodb.INFO [2023-05-26 04:11:57.948][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-05-26 04:11:57.949][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:11:57.951][biodb::testThat]
biodb.INFO [2023-05-26 04:11:58.002][biodb::testThat]
biodb.INFO [2023-05-26 04:11:58.004][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-05-26 04:11:58.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:11:58.006][biodb::testThat]
biodb.INFO [2023-05-26 04:11:58.016][biodb::testThat]
biodb.INFO [2023-05-26 04:11:58.018][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-05-26 04:11:58.019][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:11:58.020][biodb::testThat]
biodb.DEBUG[2023-05-26 04:11:58.025][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-05-26 04:11:58.029][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:11:58.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:11:58.033][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-05-26 04:12:02.314][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-05-26 04:12:18.490][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:12:18.500][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-05-26 04:12:18.539][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-05-26 04:12:19.584][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:19.586][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:19.587][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:19.588][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:19.590][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:19.591][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:19.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:19.594][ef$get] fields variable is a list.
biodb.INFO [2023-05-26 04:12:19.596][biodb::testThat]
biodb.INFO [2023-05-26 04:12:19.597][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-05-26 04:12:19.599][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:12:19.600][biodb::testThat]
biodb.ERROR[2023-05-26 04:12:19.619][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-05-26 04:12:19.639][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-05-26 04:12:19.654][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-26 04:12:19.655][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-26 04:12:19.657][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-26 04:12:19.658][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-26 04:12:19.659][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:19.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:19.662][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:19.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:19.664][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-26 04:12:19.679][biodb::testContext]
biodb.INFO [2023-05-26 04:12:19.681][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:12:19.682][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-05-26 04:12:19.683][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:12:19.685][biodb::testContext]
biodb.INFO [2023-05-26 04:12:19.691][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:12:19.694][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-26 04:12:19.699][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:12:19.700][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-26 04:12:19.702][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-26 04:12:19.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.707][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-26 04:12:19.708][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-26 04:12:19.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.713][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-26 04:12:19.715][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-26 04:12:19.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.720][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-26 04:12:19.722][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-26 04:12:19.723][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-26 04:12:19.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.728][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-26 04:12:19.730][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-26 04:12:19.731][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-26 04:12:19.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.737][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-26 04:12:19.738][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-26 04:12:19.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.743][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-26 04:12:19.745][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-26 04:12:19.746][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-26 04:12:19.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.751][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-26 04:12:19.753][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-26 04:12:19.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.758][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-26 04:12:19.760][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-26 04:12:19.761][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-26 04:12:19.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.766][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:12:19.767][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-26 04:12:19.769][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-26 04:12:19.770][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-26 04:12:19.772][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-26 04:12:19.773][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-26 04:12:19.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.778][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-26 04:12:19.780][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-26 04:12:19.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.784][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-26 04:12:19.786][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-26 04:12:19.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.791][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-26 04:12:19.792][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-26 04:12:19.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.797][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-26 04:12:19.799][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-26 04:12:19.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.804][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-26 04:12:19.805][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-26 04:12:19.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.810][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:12:19.811][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-26 04:12:19.816][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-26 04:12:19.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.821][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-26 04:12:19.822][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-26 04:12:19.824][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-26 04:12:19.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:19.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:19.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:19.829][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-26 04:12:19.831][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.833][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-26 04:12:19.834][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.836][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:19.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.838][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.840][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.841][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.842][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:12:19.844][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:19.845][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.846][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-26 04:12:19.848][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:19.849][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.851][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.852][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:12:19.852][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:12:19.852][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:12:19.852][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:12:19.852][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:12:19.853][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:19.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:19.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:19.857][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:19.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:19.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:19.861][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.862][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.864][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:19.865][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:19.866][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.868][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.869][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-26 04:12:19.872][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.873][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:12:19.874][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.876][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:19.877][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.878][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.880][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.881][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.882][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:12:19.884][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:19.885][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.887][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-26 04:12:19.888][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:19.889][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.891][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.892][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:12:19.892][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:12:19.892][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:12:19.892][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:12:19.892][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:12:19.893][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:19.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:19.896][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:19.898][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:19.899][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:19.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:19.902][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.903][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.905][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:19.906][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:19.907][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.908][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.910][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-26 04:12:19.912][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.914][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-26 04:12:19.915][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.916][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:19.918][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.919][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.921][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.922][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.923][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:12:19.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:19.926][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.927][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-26 04:12:19.929][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:19.930][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.931][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.933][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.934][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:19.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:19.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:19.938][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:19.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:19.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:19.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.943][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.944][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:19.946][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:19.947][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.948][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.950][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-26 04:12:19.952][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.954][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:12:19.955][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:19.958][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.959][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.960][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:19.963][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:12:19.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:19.966][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:19.967][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-26 04:12:19.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:19.970][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.971][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:19.973][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:19.974][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:19.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:19.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:19.978][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:19.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:20.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:20.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:20.016][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:20.017][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:20.018][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:20.019][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:20.021][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:20.022][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:12:20.024][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.061][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.DEBUG[2023-05-26 04:12:20.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.130][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-26 04:12:20.131][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-26 04:12:20.133][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-26 04:12:20.135][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-26 04:12:20.137][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:12:20.139][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-26 04:12:20.141][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-26 04:12:20.143][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-26 04:12:20.145][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-26 04:12:20.147][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-26 04:12:20.149][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:12:20.151][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-26 04:12:20.152][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-26 04:12:20.154][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-26 04:12:20.156][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-26 04:12:20.158][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:12:20.160][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-26 04:12:20.162][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-26 04:12:20.164][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:12:20.166][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-26 04:12:20.168][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-26 04:12:20.170][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-26 04:12:20.172][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-26 04:12:20.174][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-26 04:12:20.176][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-26 04:12:20.178][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-26 04:12:20.180][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-26 04:12:20.182][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-26 04:12:20.184][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-26 04:12:20.186][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-26 04:12:20.188][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-26 04:12:20.189][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-26 04:12:20.191][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-26 04:12:20.193][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-26 04:12:20.195][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-26 04:12:20.197][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-26 04:12:20.199][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-26 04:12:20.201][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-26 04:12:20.203][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-26 04:12:20.205][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-26 04:12:20.207][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-26 04:12:20.209][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-26 04:12:20.211][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-26 04:12:20.213][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-26 04:12:20.215][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-26 04:12:20.217][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-26 04:12:20.219][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-26 04:12:20.221][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-26 04:12:20.223][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-26 04:12:20.225][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-26 04:12:20.227][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-26 04:12:20.229][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-26 04:12:20.231][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-26 04:12:20.233][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-26 04:12:20.235][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-26 04:12:20.237][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-26 04:12:20.239][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-26 04:12:20.241][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-26 04:12:20.243][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-26 04:12:20.245][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-26 04:12:20.247][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-26 04:12:20.249][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-26 04:12:20.251][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-26 04:12:20.253][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-26 04:12:20.255][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-26 04:12:20.257][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-26 04:12:20.259][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:12:20.261][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:12:20.263][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-26 04:12:20.265][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-26 04:12:20.267][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-26 04:12:20.269][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-26 04:12:20.271][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-26 04:12:20.273][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-26 04:12:20.275][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-26 04:12:20.277][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-26 04:12:20.279][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-26 04:12:20.281][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-26 04:12:20.283][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-26 04:12:20.285][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-26 04:12:20.287][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-26 04:12:20.289][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-26 04:12:20.291][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-26 04:12:20.293][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-26 04:12:20.295][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:12:20.297][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:12:20.298][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.300][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.302][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[2023-05-26 04:12:20.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:20.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:20.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:20.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:20.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:20.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:20.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:20.471][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-26 04:12:20.473][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:12:20.475][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:20.477][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-26 04:12:20.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:20.479][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:20.481][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:20.482][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:20.484][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:20.485][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:20.486][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:12:20.488][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:20.489][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:20.490][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-26 04:12:20.492][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-26 04:12:20.493][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-26 04:12:20.495][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:20.496][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:12:20.496][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:12:20.497][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:20.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:20.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:20.502][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:20.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:20.504][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:20.506][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:20.507][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-26 04:12:20.507][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-26 04:12:20.508][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:20.510][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:20.511][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:20.512][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:20.514][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-26 04:12:20.516][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:12:20.521][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:12:20.522][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-26 04:12:20.524][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:12:20.526][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-26 04:12:20.528][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-26 04:12:20.529][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-26 04:12:20.531][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-26 04:12:20.532][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-26 04:12:20.535][biodb::testThat]
biodb.INFO [2023-05-26 04:12:20.536][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-05-26 04:12:20.538][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:12:20.539][biodb::testThat]
biodb.DEBUG[2023-05-26 04:12:20.544][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-05-26 04:12:20.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:12:20.551][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:12:20.554][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-05-26 04:12:21.500][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2023-05-26 04:12:22.457][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:12:22.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-05-26 04:12:22.482][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-05-26 04:12:22.497][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2023-05-26 04:12:22.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:12:22.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:12:22.505][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-05-26 04:12:23.458][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-05-26 04:12:24.422][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:12:24.431][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-05-26 04:12:24.446][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-05-26 04:12:24.460][biodb::testThat]
biodb.INFO [2023-05-26 04:12:24.462][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-05-26 04:12:24.463][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:12:24.464][biodb::testThat]
biodb.INFO [2023-05-26 04:12:24.498][biodb::testThat]
biodb.INFO [2023-05-26 04:12:24.499][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-05-26 04:12:24.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:12:24.502][biodb::testThat]
biodb.DEBUG[2023-05-26 04:12:24.506][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-05-26 04:12:24.510][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:12:24.511][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:12:24.514][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-05-26 04:12:26.291][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-05-26 04:12:27.114][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:12:27.124][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-05-26 04:12:27.139][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-05-26 04:12:27.149][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-05-26 04:12:27.153][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:12:27.155][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-05-26 04:12:27.156][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:12:27.158][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-05-26 04:12:27.165][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2023-05-26 04:12:27.169][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:12:27.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:12:27.173][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-05-26 04:12:27.945][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-05-26 04:12:28.713][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:12:28.722][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-05-26 04:12:28.737][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-05-26 04:12:28.748][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-05-26 04:12:28.753][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:12:28.754][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:12:28.756][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-05-26 04:12:30.274][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-05-26 04:12:43.595][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:12:43.605][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-05-26 04:12:43.622][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-05-26 04:12:43.782][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2023-05-26 04:12:43.788][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:12:43.789][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:12:43.792][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-05-26 04:12:45.275][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-05-26 04:12:49.322][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:12:49.333][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-05-26 04:12:49.352][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-05-26 04:12:49.495][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-26 04:12:49.497][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-26 04:12:49.499][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-26 04:12:49.500][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-26 04:12:49.501][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:49.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:49.504][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.506][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-26 04:12:49.513][biodb::testContext]
biodb.INFO [2023-05-26 04:12:49.514][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:12:49.515][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-05-26 04:12:49.517][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:12:49.518][biodb::testContext]
biodb.INFO [2023-05-26 04:12:49.525][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:12:49.527][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-26 04:12:49.532][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:12:49.534][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-26 04:12:49.535][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-26 04:12:49.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.581][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[2023-05-26 04:12:49.583][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-26 04:12:49.584][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-26 04:12:49.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.590][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-26 04:12:49.591][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-26 04:12:49.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.596][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-26 04:12:49.598][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-26 04:12:49.599][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-26 04:12:49.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.605][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-26 04:12:49.606][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-26 04:12:49.608][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-26 04:12:49.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.611][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[2023-05-26 04:12:49.613][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-26 04:12:49.614][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-26 04:12:49.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.619][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-26 04:12:49.621][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-26 04:12:49.622][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-26 04:12:49.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.627][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-26 04:12:49.629][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-26 04:12:49.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.635][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-26 04:12:49.636][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-26 04:12:49.638][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-26 04:12:49.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.643][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:12:49.644][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-26 04:12:49.646][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-26 04:12:49.647][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-26 04:12:49.649][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-26 04:12:49.650][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-26 04:12:49.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.655][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-26 04:12:49.656][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-26 04:12:49.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.662][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-26 04:12:49.663][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-26 04:12:49.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.668][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-26 04:12:49.670][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-26 04:12:49.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.673][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[2023-05-26 04:12:49.675][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-26 04:12:49.676][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-26 04:12:49.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.682][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-26 04:12:49.683][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-26 04:12:49.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.688][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:12:49.689][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-26 04:12:49.694][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-26 04:12:49.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.699][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-26 04:12:49.700][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-26 04:12:49.702][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-26 04:12:49.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.707][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-26 04:12:49.710][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.712][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-26 04:12:49.713][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.714][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:49.716][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.717][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.719][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.720][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.722][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:12:49.723][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:49.725][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.726][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-26 04:12:49.727][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:49.729][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.730][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.732][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:12:49.732][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:12:49.732][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:12:49.732][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:12:49.732][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:12:49.733][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:49.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:49.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:49.738][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:49.739][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:49.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:49.742][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.744][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:49.746][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:49.748][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.749][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.751][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-26 04:12:49.754][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.756][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:12:49.757][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.759][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:49.760][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.762][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.763][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.765][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.766][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:12:49.768][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:49.769][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.771][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-26 04:12:49.772][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:49.774][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.775][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.777][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:12:49.777][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:12:49.777][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:12:49.777][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:12:49.777][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:12:49.778][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:49.779][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:49.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:49.782][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:49.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:49.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:49.786][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.788][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.789][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:49.790][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:49.792][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.793][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.795][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-26 04:12:49.798][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.799][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-26 04:12:49.801][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.802][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:49.804][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.805][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.807][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.808][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.809][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:12:49.811][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:49.812][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.814][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-26 04:12:49.815][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:49.817][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.818][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.819][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.821][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:49.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:49.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:49.825][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:49.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:49.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:49.829][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.831][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.832][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:49.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:49.835][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.837][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.839][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-26 04:12:49.841][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.843][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:12:49.844][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.846][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:49.847][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.849][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.850][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.852][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.853][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:12:49.855][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:49.856][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.858][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-26 04:12:49.859][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:49.861][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.862][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:49.864][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.865][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:49.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:49.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:49.869][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:49.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:49.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:49.874][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:49.875][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:49.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:49.879][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:49.881][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:49.883][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:12:49.884][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.905][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[2023-05-26 04:12:49.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.951][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[2023-05-26 04:12:49.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:49.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:49.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:49.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:49.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:49.997][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[2023-05-26 04:12:49.999][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-26 04:12:50.001][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-26 04:12:50.003][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-26 04:12:50.024][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-26 04:12:50.026][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:12:50.028][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-26 04:12:50.030][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-26 04:12:50.032][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-26 04:12:50.034][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-26 04:12:50.036][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-26 04:12:50.038][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:12:50.040][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-26 04:12:50.042][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-26 04:12:50.044][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-26 04:12:50.046][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-26 04:12:50.048][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:12:50.050][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-26 04:12:50.052][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-26 04:12:50.054][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:12:50.056][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-26 04:12:50.058][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-26 04:12:50.060][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-26 04:12:50.062][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-26 04:12:50.064][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-26 04:12:50.066][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-26 04:12:50.068][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-26 04:12:50.070][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-26 04:12:50.072][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-26 04:12:50.074][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-26 04:12:50.076][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-26 04:12:50.078][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-26 04:12:50.080][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-26 04:12:50.082][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-26 04:12:50.084][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-26 04:12:50.086][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-26 04:12:50.088][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-26 04:12:50.090][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-26 04:12:50.092][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-26 04:12:50.094][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-26 04:12:50.096][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-26 04:12:50.098][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-26 04:12:50.100][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-26 04:12:50.101][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-26 04:12:50.103][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-26 04:12:50.105][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-26 04:12:50.107][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-26 04:12:50.109][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-26 04:12:50.111][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-26 04:12:50.113][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-26 04:12:50.115][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-26 04:12:50.117][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-26 04:12:50.119][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-26 04:12:50.121][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-26 04:12:50.123][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-26 04:12:50.125][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-26 04:12:50.127][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-26 04:12:50.129][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-26 04:12:50.131][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-26 04:12:50.133][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-26 04:12:50.135][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-26 04:12:50.137][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-26 04:12:50.139][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-26 04:12:50.141][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-26 04:12:50.143][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-26 04:12:50.145][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-26 04:12:50.147][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-26 04:12:50.149][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:12:50.151][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:12:50.153][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-26 04:12:50.155][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-26 04:12:50.157][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-26 04:12:50.159][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-26 04:12:50.161][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-26 04:12:50.163][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-26 04:12:50.165][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-26 04:12:50.167][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-26 04:12:50.169][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-26 04:12:50.171][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-26 04:12:50.173][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-26 04:12:50.175][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-26 04:12:50.177][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-26 04:12:50.179][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-26 04:12:50.181][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-26 04:12:50.184][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-26 04:12:50.186][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:12:50.187][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:12:50.188][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.191][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.201][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[2023-05-26 04:12:50.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.236][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[2023-05-26 04:12:50.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.245][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[2023-05-26 04:12:50.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.280][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[2023-05-26 04:12:50.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.315][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[2023-05-26 04:12:50.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:12:50.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:50.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:50.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:50.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:50.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:50.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:12:50.343][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-26 04:12:50.345][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:12:50.348][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:50.349][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-26 04:12:50.350][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:50.352][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:12:50.353][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:50.355][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:12:50.356][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:50.358][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:12:50.359][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:12:50.361][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:12:50.362][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:50.364][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-26 04:12:50.365][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-26 04:12:50.367][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-26 04:12:50.368][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-26 04:12:50.370][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:12:50.370][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:12:50.371][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:12:50.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:50.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:50.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:12:50.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:12:50.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:12:50.379][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:12:50.381][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-26 04:12:50.381][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-26 04:12:50.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:12:50.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:12:50.385][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-26 04:12:50.386][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:12:50.388][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-26 04:12:50.390][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:12:50.395][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:12:50.396][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-26 04:12:50.398][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-26 04:12:50.400][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-26 04:12:50.402][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-26 04:12:50.403][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-26 04:12:50.405][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-26 04:12:50.406][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-26 04:12:50.408][biodb::testThat]
biodb.INFO [2023-05-26 04:12:50.410][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-05-26 04:12:50.411][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:12:50.412][biodb::testThat]
biodb.DEBUG[2023-05-26 04:12:50.418][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-05-26 04:12:50.424][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:12:50.425][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-05-26 04:12:50.427][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:12:50.516][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-05-26 04:12:51.557][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-05-26 04:12:51.559][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-26 04:12:51.561][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-05-26 04:12:51.563][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-05-26 04:12:51.565][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-05-26 04:12:51.566][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:12:51.590][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-26 04:12:51.592][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-26 04:12:51.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:12:51.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:51.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:51.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:51.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:51.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:51.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:12:51.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:51.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:51.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:51.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:51.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:51.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:51.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:51.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:51.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.644][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:12:51.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:12:51.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.650][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:12:51.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:12:51.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.656][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:51.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:51.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.661][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:51.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:51.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.671][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:51.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:51.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.677][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:51.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:51.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.687][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:12:51.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:51.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.692][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:12:51.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:51.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.702][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:51.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:51.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:51.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:51.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.733][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:12:51.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.738][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-26 04:12:51.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.756][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:12:51.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:51.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:51.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:51.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:51.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:51.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:51.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.816][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:51.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:51.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:51.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:51.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:51.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:51.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:51.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:51.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:12:51.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:12:51.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:51.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:51.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:51.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:51.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:51.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:12:51.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:51.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:51.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:51.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:51.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:51.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:51.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:51.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:51.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.894][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:12:51.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-26 04:12:51.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.901][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:12:51.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:12:51.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.907][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:51.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:51.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.912][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:51.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:51.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.922][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:51.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:51.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.928][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:51.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:51.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.938][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:12:51.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:51.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.944][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-26 04:12:51.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:51.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:51.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:51.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.960][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:51.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:51.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.969][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:51.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:51.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:51.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:51.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.012][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:12:52.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.017][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-26 04:12:52.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.035][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-26 04:12:52.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.045][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.051][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:12:52.126][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-05-26 04:12:52.129][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:12:52.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:12:52.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:52.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:52.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:52.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:52.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:52.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:12:52.149][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:12:52.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:12:52.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.155][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:12:52.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:12:52.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.161][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-26 04:12:52.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-26 04:12:52.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.167][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-26 04:12:52.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-26 04:12:52.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.173][private$selectFields] Fields none
biodb.TRACE[2023-05-26 04:12:52.174][private$selectFields]
biodb.TRACE[2023-05-26 04:12:52.176][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-05-26 04:12:52.177][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:12:52.178][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:12:52.180][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.182][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.184][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.186][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.188][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.190][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.191][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.192][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.194][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.197][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.198][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.200][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.201][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.203][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.204][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.206][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.207][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.208][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.210][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.212][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.213][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.215][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.216][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.218][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.219][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.220][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.222][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.224][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.225][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.226][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.228][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.229][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.231][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.232][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.234][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.235][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.238][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.239][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.241][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.244][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.245][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.247][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.249][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.251][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.254][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.255][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.257][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.258][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.260][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.261][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.263][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.264][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.266][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.267][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.268][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.270][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.271][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.273][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.274][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:12:52.276][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:12:52.277][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.279][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.281][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.283][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.284][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.286][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.287][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.289][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.290][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.292][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.293][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.295][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.296][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.298][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.299][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.300][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.302][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.303][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.305][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.306][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.308][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.309][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.310][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.312][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.313][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.315][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.316][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.318][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.319][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.321][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.322][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.324][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-05-26 04:12:52.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.361][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.373][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.379][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.385][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.391][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.422][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.428][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.472][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.478][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.484][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.497][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-05-26 04:12:52.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:12:52.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:52.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:52.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:52.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:52.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:52.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:12:52.516][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:12:52.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:12:52.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:12:52.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:12:52.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-26 04:12:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-26 04:12:52.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.533][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-26 04:12:52.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-26 04:12:52.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.539][private$selectFields] Fields none
biodb.TRACE[2023-05-26 04:12:52.541][private$selectFields]
biodb.TRACE[2023-05-26 04:12:52.542][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-05-26 04:12:52.543][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:12:52.545][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:12:52.546][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.548][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.549][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.551][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.552][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.553][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.555][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.556][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.557][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.559][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.561][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.562][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.564][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.565][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.567][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.568][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.571][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.574][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.575][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.577][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.578][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.580][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.581][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.583][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.584][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.585][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.587][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.588][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.590][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.591][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.592][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.594][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.596][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.597][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.598][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.600][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.603][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.604][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.607][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.610][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.612][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.613][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.616][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.617][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.619][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.622][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.623][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.625][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.626][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.627][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.629][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.631][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.632][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.633][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.635][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.636][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.638][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.639][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.641][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:12:52.642][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-26 04:12:52.644][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.645][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.647][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.648][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.651][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.654][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.656][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.657][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.660][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.662][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.663][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.665][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.666][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.669][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.672][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.673][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.675][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.676][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.678][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.679][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.681][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.682][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.683][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.685][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.686][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.688][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.689][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.691][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-05-26 04:12:52.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:12:52.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:12:52.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:12:52.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.728][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.734][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.740][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-26 04:12:52.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.752][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.758][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-26 04:12:52.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:12:52.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.787][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:12:52.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:12:52.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.805][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:12:52.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:12:52.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.818][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.824][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-26 04:12:52.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:12:52.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:12:52.841][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-05-26 04:12:52.842][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:12:52.844][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-05-26 04:12:52.848][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-26 04:12:52.850][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-26 04:12:52.851][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-26 04:12:52.852][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-26 04:12:52.854][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:12:52.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:12:52.856][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:12:52.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:12:52.859][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:12:52.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 162 ]

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

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 162 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn1.3180.0404.446
LipidmapsStructureEntry0.2530.0000.254