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This page was generated on 2023-05-31 05:44:30 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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CHECK results for biodbLipidmaps on kunpeng1


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: 2023-05-29 10:19:22 -0000 (Mon, 29 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)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / 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: 2023-05-30 01:51:44 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 01:59:01 -0000 (Tue, 30 May 2023)
EllapsedTime: 436.6 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 (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 1.548  0.044  10.046
* 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 2 | WARN 0 | SKIP 0 | PASS 156 ]
  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 [2023-05-30 01:52:42.693][biodb::testContext]
biodb.INFO [2023-05-30 01:52:42.696][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:52:42.698][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-05-30 01:52:42.699][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:52:42.700][biodb::testContext]
biodb.INFO [2023-05-30 01:52:42.721][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:52:42.724][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-30 01:52:42.733][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:42.735][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-30 01:52:42.736][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-30 01:52:42.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.742][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-30 01:52:42.769][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-30 01:52:42.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.774][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-30 01:52:42.776][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-30 01:52:42.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.781][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-30 01:52:42.782][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-30 01:52:42.784][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-30 01:52:42.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.789][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-30 01:52:42.790][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-30 01:52:42.792][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-30 01:52:42.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.797][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-30 01:52:42.798][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-30 01:52:42.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.802][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[2023-05-30 01:52:42.804][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-30 01:52:42.805][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-30 01:52:42.807][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-30 01:52:42.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.812][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-30 01:52:42.813][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-30 01:52:42.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.819][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-30 01:52:42.820][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-30 01:52:42.822][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-30 01:52:42.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.827][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:52:42.828][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-30 01:52:42.830][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-30 01:52:42.832][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-30 01:52:42.834][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-30 01:52:42.835][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-30 01:52:42.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.841][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-30 01:52:42.842][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-30 01:52:42.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.847][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-30 01:52:42.849][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-30 01:52:42.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.854][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-30 01:52:42.855][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-30 01:52:42.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.861][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-30 01:52:42.862][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-30 01:52:42.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.867][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-30 01:52:42.869][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-30 01:52:42.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.874][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:52:42.876][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-30 01:52:42.880][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-30 01:52:42.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.885][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-30 01:52:42.887][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-30 01:52:42.888][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-30 01:52:42.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:42.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:42.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:42.897][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-30 01:52:42.947][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:42.981][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-30 01:52:42.982][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:42.984][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:42.985][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:42.986][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:42.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:42.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:42.990][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:52:42.992][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:42.993][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:42.995][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-30 01:52:42.996][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:42.997][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:42.999][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.000][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:43.000][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:52:43.000][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:52:43.000][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:52:43.000][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:52:43.001][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:43.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.005][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:43.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.009][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.010][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.011][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:43.013][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:43.014][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.015][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.017][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-30 01:52:43.019][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.021][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:52:43.022][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.023][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:43.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.026][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.027][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.029][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.030][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:52:43.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:43.033][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.034][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-30 01:52:43.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:43.037][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.038][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.039][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:43.039][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:52:43.039][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:52:43.039][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:52:43.039][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:52:43.042][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:43.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.046][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:43.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.050][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.051][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:43.053][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:43.055][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.056][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.058][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-30 01:52:43.060][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.061][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-30 01:52:43.063][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:43.065][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.067][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.068][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.071][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:52:43.072][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:43.074][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.075][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-30 01:52:43.076][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:43.078][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.079][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.080][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.082][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:43.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:43.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.089][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.090][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.092][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:43.093][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:43.094][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.095][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.097][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-30 01:52:43.099][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.101][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:52:43.102][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.103][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:43.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.107][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.109][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.110][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:52:43.111][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:43.113][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.114][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-30 01:52:43.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:43.117][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.118][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.119][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.121][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:43.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:43.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.129][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.131][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:43.132][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:43.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.134][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.140][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:43.141][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.219][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[2023-05-30 01:52:43.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.245][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[2023-05-30 01:52:43.246][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-30 01:52:43.252][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-30 01:52:43.256][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-30 01:52:43.258][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-30 01:52:43.260][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-30 01:52:43.262][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:52:43.264][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-30 01:52:43.266][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-30 01:52:43.267][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-30 01:52:43.269][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:52:43.271][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:52:43.273][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-30 01:52:43.275][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-30 01:52:43.277][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-30 01:52:43.279][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-30 01:52:43.281][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:52:43.282][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-30 01:52:43.284][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-30 01:52:43.286][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-30 01:52:43.288][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-30 01:52:43.290][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-30 01:52:43.292][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-30 01:52:43.294][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-30 01:52:43.296][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-30 01:52:43.298][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-30 01:52:43.299][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-30 01:52:43.301][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-30 01:52:43.303][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-30 01:52:43.305][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-30 01:52:43.307][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-30 01:52:43.309][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-30 01:52:43.318][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-30 01:52:43.320][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-30 01:52:43.322][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-30 01:52:43.324][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-30 01:52:43.326][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-30 01:52:43.328][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-30 01:52:43.330][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-30 01:52:43.332][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-30 01:52:43.334][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-30 01:52:43.335][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-30 01:52:43.337][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-30 01:52:43.339][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-30 01:52:43.341][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-30 01:52:43.343][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-30 01:52:43.345][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-30 01:52:43.347][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-30 01:52:43.349][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-30 01:52:43.351][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-30 01:52:43.353][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-30 01:52:43.355][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-30 01:52:43.357][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-30 01:52:43.359][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-30 01:52:43.360][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-30 01:52:43.362][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-30 01:52:43.364][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-30 01:52:43.366][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-30 01:52:43.368][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-30 01:52:43.370][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-30 01:52:43.372][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-30 01:52:43.374][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-30 01:52:43.376][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-30 01:52:43.378][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-30 01:52:43.380][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-30 01:52:43.382][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-30 01:52:43.384][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-30 01:52:43.386][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-30 01:52:43.387][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-30 01:52:43.389][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-30 01:52:43.391][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-30 01:52:43.393][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-30 01:52:43.395][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-30 01:52:43.397][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-30 01:52:43.399][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-30 01:52:43.401][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-30 01:52:43.403][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-30 01:52:43.405][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-30 01:52:43.407][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-30 01:52:43.409][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-30 01:52:43.411][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-30 01:52:43.412][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-30 01:52:43.414][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-30 01:52:43.416][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-30 01:52:43.424][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-30 01:52:43.426][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:52:43.431][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:43.432][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.434][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.436][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[2023-05-30 01:52:43.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.494][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[2023-05-30 01:52:43.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.502][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[2023-05-30 01:52:43.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.511][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[2023-05-30 01:52:43.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.537][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.DEBUG[2023-05-30 01:52:43.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:43.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:43.591][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-30 01:52:43.604][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:52:43.606][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.608][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:43.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.613][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.615][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.617][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:52:43.619][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:43.620][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.621][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-30 01:52:43.623][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-30 01:52:43.624][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-30 01:52:43.626][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:43.627][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:43.627][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:52:43.629][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:43.630][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.631][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.633][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:43.634][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:43.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:43.637][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:43.638][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-30 01:52:43.638][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-30 01:52:43.639][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:43.641][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:43.642][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:43.643][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:43.653][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-30 01:52:43.662][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:52:43.694][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:52:43.695][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-30 01:52:43.701][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:52:43.706][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-30 01:52:43.712][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-30 01:52:43.714][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-30 01:52:43.715][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-30 01:52:43.717][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-30 01:52:43.738][biodb::testThat]
biodb.INFO [2023-05-30 01:52:43.740][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-05-30 01:52:43.741][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:43.743][biodb::testThat]
biodb.TRACE[2023-05-30 01:52:43.748][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[2023-05-30 01:52:43.754][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:52:43.759][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-30 01:52:43.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:43.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:43.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:43.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:43.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:43.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:43.794][FUN] Functions in observer BiodbConfig: [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[2023-05-30 01:52:43.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:43.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:43.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:43.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:43.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:43.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:43.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.848][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:43.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:43.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.855][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:43.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:43.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.861][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:43.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:43.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.902][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:43.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:43.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.911][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:43.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:43.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.917][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:43.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:43.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.926][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:52:43.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:43.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.932][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:52:43.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:43.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.941][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:43.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:43.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:43.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:43.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:43.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:43.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:43.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:43.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.971][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:52:43.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:43.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.977][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-30 01:52:43.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:43.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:43.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:43.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:43.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:43.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:43.994][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:52:43.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:43.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:43.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.117][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.123][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.133][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:44.176][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-05-30 01:52:44.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:52:44.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:52:44.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:52:44.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:52:44.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.194][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-30 01:52:44.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-30 01:52:44.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.199][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-30 01:52:44.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-30 01:52:44.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.295][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.306][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.347][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.349][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.351][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.386][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.387][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.388][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.390][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.406][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.423][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.425][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.426][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.428][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.444][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:44.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:44.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:44.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:44.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:44.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:44.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.462][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:44.464][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:44.465][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.466][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.468][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:44.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:44.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.501][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.503][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.504][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.532][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.538][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.539][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.541][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.542][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.559][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.560][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.562][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.563][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.571][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.572][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.574][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.575][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.583][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:44.584][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:44.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.587][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.597][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.598][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.599][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.607][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.609][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.610][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.612][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.620][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.621][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.624][ef$get] fields variable is a list.
biodb.INFO [2023-05-30 01:52:44.633][biodb::testThat]
biodb.INFO [2023-05-30 01:52:44.634][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-05-30 01:52:44.636][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:44.637][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:44.692][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-05-30 01:52:44.702][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-30 01:52:44.707][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-05-30 01:52:44.709][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:52:44.711][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-05-30 01:52:44.713][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:52:44.778][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:52:44.779][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-30 01:52:44.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:44.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:44.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:44.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:44.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:44.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:44.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:52:44.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:44.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:44.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:44.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:44.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:44.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:44.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.832][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:44.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:44.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.837][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:44.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:44.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.843][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.849][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:44.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.864][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:44.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.874][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:52:44.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.880][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:52:44.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:44.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.889][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:44.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:44.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:44.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:44.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.904][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.919][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:52:44.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.925][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-30 01:52:44.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.941][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:52:44.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:44.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:44.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.991][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:44.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:44.997][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:44.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:45.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:45.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.008][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:45.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:52:45.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:45.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:45.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:45.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:45.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:45.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:45.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:45.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:45.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:45.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:45.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:45.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:45.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:45.051][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-05-30 01:52:45.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-05-30 01:52:45.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-05-30 01:52:45.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-05-30 01:52:45.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-05-30 01:52:45.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-05-30 01:52:45.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-05-30 01:52:45.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-30 01:52:45.079][biodb::testThat]
biodb.INFO [2023-05-30 01:52:45.080][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-05-30 01:52:45.081][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:45.083][biodb::testThat]
biodb.TRACE[2023-05-30 01:52:45.087][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:45.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:45.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.091][ef$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:45.093][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-05-30 01:52:45.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:45.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:45.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:45.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:45.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:45.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:45.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:45.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:45.150][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-30 01:52:45.168][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[2023-05-30 01:52:45.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:52:45.198][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:52:45.200][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-05-30 01:52:46.378][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-05-30 01:52:47.449][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:52:47.459][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-05-30 01:52:47.489][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-05-30 01:52:47.495][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-05-30 01:52:47.515][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:47.516][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:47.517][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.519][ef$get] fields variable is a list.
biodb.INFO [2023-05-30 01:52:47.521][biodb::testThat]
biodb.INFO [2023-05-30 01:52:47.523][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-05-30 01:52:47.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:47.525][biodb::testThat]
biodb.TRACE[2023-05-30 01:52:47.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:47.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:47.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:47.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:47.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:47.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:47.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:47.742][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-30 01:52:47.746][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-30 01:52:47.768][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-30 01:52:47.770][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:52:47.772][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-05-30 01:52:47.801][biodb::testThat]
biodb.INFO [2023-05-30 01:52:47.802][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-05-30 01:52:47.804][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:47.805][biodb::testThat]
biodb.TRACE[2023-05-30 01:52:47.839][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:52:47.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:52:47.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.845][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:52:47.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:52:47.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.850][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-30 01:52:47.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-30 01:52:47.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.855][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-30 01:52:47.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-30 01:52:47.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.921][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:52:47.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:52:47.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.926][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:52:47.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:52:47.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.931][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-30 01:52:47.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-30 01:52:47.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:47.937][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-30 01:52:47.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-30 01:52:47.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:47.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-30 01:52:47.945][biodb::testThat]
biodb.INFO [2023-05-30 01:52:47.946][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-05-30 01:52:47.947][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:47.949][biodb::testThat]
biodb.INFO [2023-05-30 01:52:47.955][biodb::testThat]
biodb.INFO [2023-05-30 01:52:47.956][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-05-30 01:52:47.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:47.959][biodb::testThat]
biodb.INFO [2023-05-30 01:52:47.965][biodb::testThat]
biodb.INFO [2023-05-30 01:52:47.966][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-05-30 01:52:47.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:47.968][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:47.973][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-05-30 01:52:50.896][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-05-30 01:52:51.753][biodb::testThat]
biodb.INFO [2023-05-30 01:52:51.754][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-05-30 01:52:51.756][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:51.757][biodb::testThat]
biodb.TRACE[2023-05-30 01:52:51.787][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:51.789][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:51.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:51.791][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:51.793][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:51.794][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:51.796][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:51.797][ef$get] fields variable is a list.
biodb.INFO [2023-05-30 01:52:51.799][biodb::testThat]
biodb.INFO [2023-05-30 01:52:51.801][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-05-30 01:52:51.802][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:51.804][biodb::testThat]
biodb.TRACE[2023-05-30 01:52:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:51.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:51.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:51.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:51.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:51.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:51.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:51.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:51.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:51.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:51.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:51.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:51.963][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-30 01:52:51.968][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-30 01:52:51.969][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-30 01:52:51.971][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:52:51.973][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-05-30 01:52:52.085][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-30 01:52:52.090][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-30 01:52:52.092][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-30 01:52:52.094][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:52:52.095][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-05-30 01:52:52.117][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:52.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:52.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:52.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:52.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-30 01:52:52.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-30 01:52:52.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:52.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:52.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:52.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:52.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:52.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:52.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:52.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:52.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:52.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:52.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:52.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:52.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:52.228][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-05-30 01:52:52.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:52:52.251][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:52:52.281][private$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[2023-05-30 01:52:59.993][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[2023-05-30 01:53:59.305][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:53:59.314][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-05-30 01:53:59.353][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-05-30 01:54:00.615][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[2023-05-30 01:54:00.620][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:54:00.622][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:54:00.625][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-05-30 01:54:05.000][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-05-30 01:54:06.090][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:54:06.100][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-05-30 01:54:06.117][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-05-30 01:54:06.220][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-05-30 01:54:06.225][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:54:06.226][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:54:06.229][private$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[2023-05-30 01:54:07.273][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[2023-05-30 01:54:08.345][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:54:08.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-05-30 01:54:08.370][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-05-30 01:54:08.403][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-30 01:54:08.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-30 01:54:08.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:54:08.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-30 01:54:08.424][biodb::testThat]
biodb.INFO [2023-05-30 01:54:08.425][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-05-30 01:54:08.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:54:08.428][biodb::testThat]
biodb.TRACE[2023-05-30 01:54:08.433][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:54:08.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:54:08.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:54:08.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:54:08.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-30 01:54:08.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-30 01:54:08.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:54:08.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:54:08.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:54:08.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:54:08.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:54:08.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:54:08.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:54:08.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:54:08.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:54:08.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:54:08.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:54:08.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:54:08.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:54:08.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:54:08.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:54:08.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:54:08.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:54:08.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:54:08.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:54:08.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:54:08.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:54:08.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:54:08.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:54:08.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:54:08.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:54:08.566][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[2023-05-30 01:54:08.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:54:08.572][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:54:08.575][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-05-30 01:54:12.861][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.INFO [2023-05-30 01:55:12.921][biodb::testThat]
biodb.INFO [2023-05-30 01:55:12.923][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-05-30 01:55:12.924][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:55:12.925][biodb::testThat]
biodb.TRACE[2023-05-30 01:55:12.950][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:55:12.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:55:12.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:55:12.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:55:12.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-30 01:55:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-30 01:55:12.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:55:12.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:55:12.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:55:12.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:55:12.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:55:12.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:55:12.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:55:12.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:55:12.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:55:12.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:55:12.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:55:12.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:55:12.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:55:12.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:55:12.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:55:12.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:55:12.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:55:12.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:55:13.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:55:13.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:55:13.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:55:13.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:55:13.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:55:13.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:55:13.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:55:13.159][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2023-05-30 01:55:13.164][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:55:13.165][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:55:13.168][private$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[2023-05-30 01:55:17.520][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 [2023-05-30 01:56:17.599][biodb::testThat]
biodb.INFO [2023-05-30 01:56:17.601][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-05-30 01:56:17.603][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:56:17.604][biodb::testThat]
biodb.TRACE[2023-05-30 01:56:17.609][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:56:17.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:56:17.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:17.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:17.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-30 01:56:17.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-30 01:56:17.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:17.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:17.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:17.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:17.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:17.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:17.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:17.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:17.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:17.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:17.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:17.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:17.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:17.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:17.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:17.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:17.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:17.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:56:17.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:17.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:17.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:17.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:17.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:17.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:17.673][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[2023-05-30 01:56:17.758][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[2023-05-30 01:56:17.763][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:56:17.765][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:56:17.767][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-05-30 01:56:22.162][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-05-30 01:56:46.983][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:56:46.994][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-05-30 01:56:47.034][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-05-30 01:56:48.196][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-05-30 01:56:48.268][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-30 01:56:48.272][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-05-30 01:56:48.274][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-05-30 01:56:48.276][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-30 01:56:48.277][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:56:48.279][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-30 01:56:48.281][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-30 01:56:48.282][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-30 01:56:48.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:48.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:48.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:48.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:48.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:48.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:48.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:56:48.324][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-05-30 01:56:48.328][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:56:48.329][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:56:48.332][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-05-30 01:56:49.381][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-05-30 01:56:50.476][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:56:50.486][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-05-30 01:56:50.501][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-05-30 01:56:50.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:50.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:50.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:50.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:50.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:50.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:50.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:56:50.523][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-05-30 01:56:50.527][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:56:50.528][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:56:50.530][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-05-30 01:56:51.597][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-05-30 01:56:57.690][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:56:57.699][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-05-30 01:56:57.714][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-05-30 01:56:57.728][private$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[2023-05-30 01:56:57.734][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-30 01:56:57.760][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-30 01:56:57.766][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-30 01:56:57.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:57.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:57.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:57.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:57.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:57.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:57.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:56:57.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:57.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:57.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:57.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:57.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:56:57.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:56:57.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:56:57.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:56:57.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.859][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:56:57.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:56:57.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.865][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:56:57.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:56:57.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.871][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:56:57.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:56:57.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.877][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:56:57.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:56:57.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.887][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:56:57.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:56:57.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.893][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:56:57.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:56:57.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.903][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:56:57.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:57.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.909][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:56:57.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:57.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.919][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:56:57.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:56:57.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.926][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:56:57.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:56:57.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:56:57.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:57.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:56:57.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:57.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.951][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:56:57.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:57.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.958][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-30 01:56:57.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:57.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:56:57.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:57.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:56:57.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:57.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.976][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:56:57.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:57.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:57.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:57.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.992][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:57.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:57.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:57.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:57.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:57.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.004][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:56:58.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:58.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:58.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:58.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:58.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:58.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:58.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:56:58.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:56:58.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:56:58.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.108][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:56:58.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:56:58.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.114][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:56:58.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:56:58.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.120][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:56:58.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:56:58.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.125][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:56:58.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:56:58.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.135][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:56:58.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:56:58.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.141][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:56:58.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:56:58.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.151][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:56:58.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:58.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.156][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:56:58.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:56:58.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.166][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:56:58.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:56:58.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.172][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:56:58.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:56:58.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.181][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:56:58.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:58.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:56:58.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:58.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.196][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:56:58.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:58.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-30 01:56:58.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:58.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.208][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:56:58.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:58.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:56:58.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:58.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.220][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:56:58.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:56:58.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.229][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.235][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:56:58.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:56:58.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:56:58.324][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-05-30 01:56:58.338][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-30 01:56:58.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:58.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:58.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:58.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:58.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:58.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:58.355][FUN] Functions in observer BiodbConfig: [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[2023-05-30 01:56:58.357][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.362][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.368][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.370][private$selectFields]
biodb.TRACE[2023-05-30 01:56:58.371][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-30 01:56:58.372][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-30 01:56:58.374][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.375][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.377][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.378][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.379][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.381][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.382][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.384][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.385][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.387][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.388][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.389][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.391][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.392][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.394][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.395][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-30 01:56:58.397][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.402][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.408][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.427][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-05-30 01:56:58.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:58.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:58.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:58.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:58.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:58.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:58.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:56:58.446][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.452][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.458][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.460][private$selectFields]
biodb.TRACE[2023-05-30 01:56:58.461][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-30 01:56:58.462][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-30 01:56:58.464][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.466][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.467][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.469][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.470][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.472][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.473][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.475][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.476][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.477][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.479][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.480][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.482][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.483][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.485][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.486][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-30 01:56:58.488][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.494][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.499][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.521][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-05-30 01:56:58.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:58.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:58.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:58.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:58.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:58.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:58.537][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[2023-05-30 01:56:58.539][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.551][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.552][private$selectFields]
biodb.TRACE[2023-05-30 01:56:58.553][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-30 01:56:58.555][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-30 01:56:58.556][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.557][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.559][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.560][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.562][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.563][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.564][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.566][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.567][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.568][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.570][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:56:58.571][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.573][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.574][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.575][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.577][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-30 01:56:58.578][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.584][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:56:58.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:56:58.595][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-05-30 01:56:58.597][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-30 01:56:58.598][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-30 01:56:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-30 01:56:58.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-30 01:56:58.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:56:58.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-30 01:56:58.637][biodb::testThat]
biodb.INFO [2023-05-30 01:56:58.639][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-05-30 01:56:58.640][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:56:58.641][biodb::testThat]
biodb.DEBUG[2023-05-30 01:56:58.644][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-05-30 01:56:58.646][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-30 01:56:58.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-05-30 01:56:58.650][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-30 01:56:58.651][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-30 01:56:58.653][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:56:58.654][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-30 01:56:58.656][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-30 01:56:58.657][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-30 01:56:58.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:56:58.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:56:58.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:56:58.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:56:58.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:56:58.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:56:58.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:56:58.693][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-05-30 01:56:58.696][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:56:58.698][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:56:58.700][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:56:59.757][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:56:59.787][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:56:59.792][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[2023-05-30 01:56:59.794][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:02.760][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:02.761][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:02.763][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:02.765][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:03.796][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:03.798][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:03.800][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[2023-05-30 01:57:03.801][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:04.981][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:04.983][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:04.984][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:04.986][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:06.022][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:06.024][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:06.026][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[2023-05-30 01:57:06.028][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:07.186][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:07.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:07.189][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:07.191][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:08.235][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:08.237][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:08.239][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[2023-05-30 01:57:08.240][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:09.400][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:09.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:09.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:09.405][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:10.399][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:10.400][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:10.402][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[2023-05-30 01:57:10.403][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:11.596][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:11.598][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:11.599][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:11.601][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:12.612][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:12.613][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:12.615][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[2023-05-30 01:57:12.616][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:13.775][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:13.777][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:13.778][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:13.780][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:14.803][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:14.805][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:14.806][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[2023-05-30 01:57:14.807][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:15.976][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:15.978][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:15.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:15.982][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:16.986][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:16.988][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:16.989][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[2023-05-30 01:57:16.991][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:18.220][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:18.222][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:18.224][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:18.225][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:19.241][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:19.243][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:19.244][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[2023-05-30 01:57:19.246][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:21.187][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-30 01:57:21.188][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:21.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:21.192][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-30 01:57:22.240][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:22.241][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:22.243][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[2023-05-30 01:57:22.244][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-30 01:57:23.401][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2023-05-30 01:57:23.412][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-05-30 01:57:23.417][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-30 01:57:23.441][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:57:23.443][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-30 01:57:23.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:57:23.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:57:23.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:57:23.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:57:23.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:57:23.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:57:23.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:57:23.463][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:23.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:23.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:23.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:23.469][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:23.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:23.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:23.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:23.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:23.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:23.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:23.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:23.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:23.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:23.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:23.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:23.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:23.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:23.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:23.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:23.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:23.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:23.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:23.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:23.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:23.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:23.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:23.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:23.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:23.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:23.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:57:23.509][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-05-30 01:57:23.510][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-05-30 01:57:23.519][biodb::testThat]
biodb.INFO [2023-05-30 01:57:23.520][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-05-30 01:57:23.522][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:57:23.523][biodb::testThat]
biodb.DEBUG[2023-05-30 01:57:23.534][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-05-30 01:57:23.535][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-05-30 01:57:23.536][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-30 01:57:23.539][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-05-30 01:57:23.540][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-05-30 01:57:23.542][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-30 01:57:23.543][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:57:23.545][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-30 01:57:23.546][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-30 01:57:23.547][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-30 01:57:23.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:57:23.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:57:23.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:57:23.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:57:23.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:57:23.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:57:23.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:57:23.569][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-05-30 01:57:23.572][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:23.574][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:23.575][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:24.631][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:24.632][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:24.633][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:24.635][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:25.806][private$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[2023-05-30 01:57:25.808][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:25.810][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:25.812][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:26.819][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:26.820][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:26.822][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:26.823][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:27.986][private$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[2023-05-30 01:57:27.987][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:27.989][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:27.991][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:29.027][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:29.028][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:29.030][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:29.031][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:30.190][private$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[2023-05-30 01:57:30.191][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:30.193][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:30.195][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:31.215][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:31.216][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:31.218][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:31.219][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:32.378][private$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[2023-05-30 01:57:32.379][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:32.381][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:32.383][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:33.414][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:33.416][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:33.417][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:33.419][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:34.613][private$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[2023-05-30 01:57:34.615][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:34.616][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:34.618][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:35.621][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:35.622][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:35.624][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:35.625][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:36.785][private$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[2023-05-30 01:57:36.786][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:36.788][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:36.789][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:37.833][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:37.835][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:37.837][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:37.838][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:39.012][private$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[2023-05-30 01:57:39.013][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:39.015][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:39.017][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:40.037][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:40.038][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:40.040][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:40.041][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:41.210][private$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[2023-05-30 01:57:41.211][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:41.213][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:41.215][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:42.234][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:42.236][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:42.238][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:42.240][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:43.403][private$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[2023-05-30 01:57:43.437][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:43.438][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:43.440][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-30 01:57:44.451][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-30 01:57:44.452][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-30 01:57:44.454][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-30 01:57:44.455][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-30 01:57:45.621][private$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[2023-05-30 01:57:45.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:57:45.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:57:45.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:57:45.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:57:45.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:57:45.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:57:45.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:57:45.640][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-05-30 01:57:45.644][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:45.646][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:45.648][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-05-30 01:57:46.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-05-30 01:57:47.809][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:57:47.818][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-05-30 01:57:47.832][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-05-30 01:57:47.845][private$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[2023-05-30 01:57:47.850][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-30 01:57:47.875][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-30 01:57:47.876][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-30 01:57:47.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:57:47.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:57:47.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:57:47.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:57:47.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:57:47.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:57:47.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:57:47.919][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:47.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:47.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:47.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:47.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:47.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:47.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:47.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:47.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:47.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:47.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:47.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:57:47.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:57:47.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:57:47.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:57:47.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:57:47.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:57:47.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:57:47.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:57:47.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:47.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:47.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:47.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:47.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:47.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:47.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:47.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:57:47.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:57:47.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:47.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:47.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:57:47.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:57:47.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:47.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:47.990][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:57:47.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:57:47.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:47.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:47.996][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:57:47.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:57:47.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.005][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:57:48.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:57:48.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.011][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:57:48.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:57:48.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.021][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:57:48.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:57:48.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.027][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:57:48.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:57:48.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.037][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:57:48.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:57:48.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:57:48.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:57:48.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.052][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:57:48.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:57:48.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.058][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:57:48.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:57:48.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:57:48.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:57:48.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.074][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:57:48.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:57:48.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.101][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:57:48.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.107][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-30 01:57:48.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.141][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:57:48.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:57:48.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:57:48.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.183][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:48.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:48.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.189][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:48.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:48.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.201][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:48.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:57:48.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:57:48.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:57:48.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:57:48.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:57:48.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:57:48.274][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-05-30 01:57:48.275][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-05-30 01:57:48.277][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-05-30 01:57:48.293][biodb::testThat]
biodb.INFO [2023-05-30 01:57:48.295][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-05-30 01:57:48.297][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:57:48.299][biodb::testThat]
biodb.INFO [2023-05-30 01:57:48.328][biodb::testThat]
biodb.INFO [2023-05-30 01:57:48.329][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-05-30 01:57:48.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:57:48.332][biodb::testThat]
biodb.INFO [2023-05-30 01:57:48.359][biodb::testThat]
biodb.INFO [2023-05-30 01:57:48.361][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-05-30 01:57:48.363][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:57:48.364][biodb::testThat]
biodb.DEBUG[2023-05-30 01:57:48.369][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-05-30 01:57:48.373][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:57:48.375][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:57:48.377][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-05-30 01:57:52.700][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-05-30 01:58:04.166][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:58:04.177][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-05-30 01:58:04.220][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-05-30 01:58:05.525][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:05.527][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:05.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:05.529][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:05.531][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:05.532][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:05.533][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:05.535][ef$get] fields variable is a list.
biodb.INFO [2023-05-30 01:58:05.537][biodb::testThat]
biodb.INFO [2023-05-30 01:58:05.538][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-05-30 01:58:05.539][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:58:05.541][biodb::testThat]
biodb.ERROR[2023-05-30 01:58:05.559][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-05-30 01:58:05.580][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-05-30 01:58:05.594][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-30 01:58:05.596][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-30 01:58:05.597][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-30 01:58:05.599][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-30 01:58:05.600][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:05.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:05.602][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:05.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:05.605][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-30 01:58:05.619][biodb::testContext]
biodb.INFO [2023-05-30 01:58:05.621][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:58:05.622][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-05-30 01:58:05.623][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:58:05.624][biodb::testContext]
biodb.INFO [2023-05-30 01:58:05.631][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:58:05.633][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-30 01:58:05.638][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:58:05.639][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-30 01:58:05.640][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-30 01:58:05.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.645][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-30 01:58:05.647][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-30 01:58:05.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.652][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-30 01:58:05.653][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-30 01:58:05.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.658][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-30 01:58:05.660][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-30 01:58:05.661][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-30 01:58:05.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.666][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-30 01:58:05.667][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-30 01:58:05.669][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-30 01:58:05.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.674][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-30 01:58:05.675][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-30 01:58:05.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.680][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-30 01:58:05.681][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-30 01:58:05.683][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-30 01:58:05.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.688][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-30 01:58:05.689][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-30 01:58:05.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.694][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-30 01:58:05.696][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-30 01:58:05.697][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-30 01:58:05.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.735][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:58:05.736][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-30 01:58:05.737][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-30 01:58:05.738][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-30 01:58:05.740][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-30 01:58:05.741][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-30 01:58:05.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.746][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-30 01:58:05.747][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-30 01:58:05.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.752][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-30 01:58:05.753][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-30 01:58:05.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.757][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[2023-05-30 01:58:05.758][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-30 01:58:05.759][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-30 01:58:05.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.764][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-30 01:58:05.765][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-30 01:58:05.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.770][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-30 01:58:05.771][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-30 01:58:05.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.776][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:58:05.777][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-30 01:58:05.781][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-30 01:58:05.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.786][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-30 01:58:05.788][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-30 01:58:05.789][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-30 01:58:05.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.794][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-30 01:58:05.796][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.798][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-30 01:58:05.799][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.800][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:05.802][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.803][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.804][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.805][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.807][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:58:05.808][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:05.809][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.811][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-30 01:58:05.812][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:05.813][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.814][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.816][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:58:05.816][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:58:05.816][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:58:05.816][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:58:05.816][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:58:05.817][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:05.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:05.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:05.821][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:05.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:05.823][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:05.824][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.826][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.827][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:05.828][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:05.829][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.831][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.832][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-30 01:58:05.835][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.836][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:58:05.837][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.839][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:05.840][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.841][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.843][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.844][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.845][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:58:05.847][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:05.848][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.849][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-30 01:58:05.850][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:05.852][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.853][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:58:05.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:58:05.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:58:05.854][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:58:05.854][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:58:05.856][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:05.857][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:05.858][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:05.859][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:05.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:05.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:05.864][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.865][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.866][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:05.868][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:05.869][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.870][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.872][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-30 01:58:05.874][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.875][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-30 01:58:05.877][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.878][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:05.879][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.881][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.882][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.883][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.885][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:58:05.886][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:05.887][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.889][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-30 01:58:05.890][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:05.891][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.892][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.894][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.895][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:05.896][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:05.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:05.899][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:05.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:05.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:05.903][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.904][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.905][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:05.907][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:05.908][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.909][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.911][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-30 01:58:05.913][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.915][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:58:05.916][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.917][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:05.919][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.920][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.921][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.923][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.924][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:58:05.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:05.926][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.928][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-30 01:58:05.942][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:05.943][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.945][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:05.946][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.947][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:05.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:05.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:05.951][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:05.952][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:05.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:05.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:05.956][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.957][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:05.959][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:05.960][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:05.961][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:05.963][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:58:05.964][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:05.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:05.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.971][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[2023-05-30 01:58:05.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:05.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:05.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:05.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:05.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:05.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:05.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:05.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:05.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:05.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:05.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:05.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:05.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:05.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.031][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[2023-05-30 01:58:06.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.037][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[2023-05-30 01:58:06.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.080][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-30 01:58:06.082][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-30 01:58:06.084][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-30 01:58:06.086][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-30 01:58:06.089][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-30 01:58:06.091][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:58:06.093][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-30 01:58:06.095][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-30 01:58:06.097][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-30 01:58:06.099][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:58:06.101][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:58:06.103][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-30 01:58:06.105][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-30 01:58:06.107][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-30 01:58:06.109][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-30 01:58:06.111][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:58:06.113][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-30 01:58:06.116][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-30 01:58:06.118][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-30 01:58:06.120][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-30 01:58:06.122][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-30 01:58:06.124][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-30 01:58:06.126][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-30 01:58:06.129][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-30 01:58:06.131][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-30 01:58:06.133][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-30 01:58:06.135][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-30 01:58:06.137][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-30 01:58:06.140][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-30 01:58:06.142][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-30 01:58:06.144][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-30 01:58:06.146][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-30 01:58:06.148][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-30 01:58:06.150][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-30 01:58:06.152][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-30 01:58:06.177][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-30 01:58:06.179][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-30 01:58:06.181][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-30 01:58:06.183][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-30 01:58:06.185][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-30 01:58:06.187][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-30 01:58:06.189][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-30 01:58:06.191][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-30 01:58:06.193][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-30 01:58:06.195][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-30 01:58:06.197][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-30 01:58:06.199][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-30 01:58:06.201][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-30 01:58:06.203][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-30 01:58:06.205][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-30 01:58:06.207][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-30 01:58:06.209][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-30 01:58:06.211][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-30 01:58:06.213][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-30 01:58:06.215][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-30 01:58:06.217][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-30 01:58:06.219][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-30 01:58:06.221][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-30 01:58:06.223][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-30 01:58:06.225][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-30 01:58:06.227][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-30 01:58:06.229][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-30 01:58:06.231][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-30 01:58:06.233][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-30 01:58:06.235][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-30 01:58:06.237][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-30 01:58:06.239][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-30 01:58:06.241][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-30 01:58:06.243][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-30 01:58:06.245][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-30 01:58:06.247][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-30 01:58:06.249][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-30 01:58:06.251][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-30 01:58:06.253][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-30 01:58:06.255][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-30 01:58:06.257][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-30 01:58:06.259][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-30 01:58:06.261][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-30 01:58:06.263][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-30 01:58:06.265][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-30 01:58:06.268][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-30 01:58:06.270][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-30 01:58:06.272][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-30 01:58:06.274][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-30 01:58:06.276][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:58:06.277][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:58:06.278][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.281][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.315][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[2023-05-30 01:58:06.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.323][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[2023-05-30 01:58:06.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:06.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:06.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:06.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:06.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:06.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:06.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:06.439][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-30 01:58:06.441][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:58:06.443][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:06.445][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-30 01:58:06.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:06.447][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:06.449][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:06.450][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:06.451][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:06.452][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:06.454][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:58:06.455][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:06.457][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:06.458][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-30 01:58:06.459][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-30 01:58:06.460][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-30 01:58:06.462][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:06.463][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:58:06.463][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:58:06.465][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:06.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:06.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:06.468][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:06.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:06.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:06.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:06.474][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-30 01:58:06.474][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-30 01:58:06.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:06.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:06.478][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:06.479][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:06.481][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-30 01:58:06.483][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:58:06.487][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:58:06.489][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-30 01:58:06.490][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:58:06.492][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-30 01:58:06.494][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-30 01:58:06.495][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-30 01:58:06.497][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-30 01:58:06.498][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-30 01:58:06.500][biodb::testThat]
biodb.INFO [2023-05-30 01:58:06.501][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-05-30 01:58:06.502][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:58:06.504][biodb::testThat]
biodb.DEBUG[2023-05-30 01:58:06.509][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[2023-05-30 01:58:06.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:58:06.516][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:58:06.518][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-05-30 01:58:07.579][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2023-05-30 01:58:08.655][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:58:08.664][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-05-30 01:58:08.697][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-05-30 01:58:08.713][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2023-05-30 01:58:08.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:58:08.720][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:58:08.723][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-05-30 01:58:09.793][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[2023-05-30 01:58:10.889][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:58:10.898][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-05-30 01:58:10.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-05-30 01:58:10.928][biodb::testThat]
biodb.INFO [2023-05-30 01:58:10.930][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-05-30 01:58:10.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:58:10.932][biodb::testThat]
biodb.INFO [2023-05-30 01:58:10.968][biodb::testThat]
biodb.INFO [2023-05-30 01:58:10.969][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-05-30 01:58:10.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:58:10.972][biodb::testThat]
biodb.DEBUG[2023-05-30 01:58:10.976][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[2023-05-30 01:58:10.981][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:58:10.982][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:58:10.984][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-05-30 01:58:11.908][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-05-30 01:58:12.801][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:58:12.811][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-05-30 01:58:12.828][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-05-30 01:58:12.838][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-05-30 01:58:12.842][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-30 01:58:12.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-05-30 01:58:12.846][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:58:12.848][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-05-30 01:58:12.854][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2023-05-30 01:58:12.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:58:12.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:58:12.863][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-05-30 01:58:13.781][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[2023-05-30 01:58:14.664][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:58:14.674][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-05-30 01:58:14.690][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-05-30 01:58:14.701][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[2023-05-30 01:58:14.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:58:14.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:58:14.710][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-05-30 01:58:16.381][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-05-30 01:58:20.707][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:58:20.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-05-30 01:58:20.742][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-05-30 01:58:20.901][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2023-05-30 01:58:20.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-30 01:58:20.907][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-30 01:58:20.909][private$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[2023-05-30 01:58:22.557][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[2023-05-30 01:58:27.039][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-30 01:58:27.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-05-30 01:58:27.068][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-05-30 01:58:27.216][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-30 01:58:27.218][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-30 01:58:27.220][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-30 01:58:27.221][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-30 01:58:27.222][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:27.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:27.225][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.255][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-30 01:58:27.261][biodb::testContext]
biodb.INFO [2023-05-30 01:58:27.263][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:58:27.264][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-05-30 01:58:27.266][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:58:27.267][biodb::testContext]
biodb.INFO [2023-05-30 01:58:27.273][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:58:27.276][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-30 01:58:27.281][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:58:27.282][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-30 01:58:27.284][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-30 01:58:27.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.290][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-30 01:58:27.292][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-30 01:58:27.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.298][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-30 01:58:27.299][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-30 01:58:27.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.305][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-30 01:58:27.306][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-30 01:58:27.308][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-30 01:58:27.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.313][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-30 01:58:27.315][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-30 01:58:27.316][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-30 01:58:27.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.326][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-30 01:58:27.328][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-30 01:58:27.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.334][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-30 01:58:27.336][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-30 01:58:27.338][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-30 01:58:27.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.344][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-30 01:58:27.345][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-30 01:58:27.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.351][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-30 01:58:27.353][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-30 01:58:27.355][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-30 01:58:27.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.360][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:58:27.362][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-30 01:58:27.364][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-30 01:58:27.365][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-30 01:58:27.367][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-30 01:58:27.368][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-30 01:58:27.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.374][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-30 01:58:27.376][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-30 01:58:27.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.382][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-30 01:58:27.383][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-30 01:58:27.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.389][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-30 01:58:27.391][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-30 01:58:27.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.397][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-30 01:58:27.399][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-30 01:58:27.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.404][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-30 01:58:27.406][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-30 01:58:27.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.412][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:58:27.414][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-30 01:58:27.418][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-30 01:58:27.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.424][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-30 01:58:27.426][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-30 01:58:27.428][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-30 01:58:27.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.434][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-30 01:58:27.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.438][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-30 01:58:27.440][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.441][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:27.443][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.446][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.448][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.449][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:58:27.451][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:27.453][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.455][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-30 01:58:27.456][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:27.458][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.460][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.461][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:58:27.461][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:58:27.461][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:58:27.461][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:58:27.461][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:58:27.463][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:27.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:27.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:27.467][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:27.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:27.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:27.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.474][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:27.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:27.479][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.480][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.482][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-30 01:58:27.485][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.487][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:58:27.539][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.541][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:27.542][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.544][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.545][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.547][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.548][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:58:27.550][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:27.551][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.553][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-30 01:58:27.554][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:27.556][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.557][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.559][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:58:27.559][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:58:27.559][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:58:27.559][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:58:27.559][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:58:27.560][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:27.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:27.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:27.564][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:27.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:27.567][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:27.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.570][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.571][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:27.573][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:27.574][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.576][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.577][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-30 01:58:27.580][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.581][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-30 01:58:27.583][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.584][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:27.586][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.587][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.589][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.590][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.592][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:58:27.593][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:27.595][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.596][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-30 01:58:27.597][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:27.599][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.600][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.602][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.603][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:27.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:27.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:27.607][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:27.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:27.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:27.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.612][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.614][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:27.615][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:27.616][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.618][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.619][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-30 01:58:27.622][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.623][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:58:27.625][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.626][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:27.627][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.629][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.630][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.632][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.633][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:58:27.634][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:27.636][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.637][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-30 01:58:27.639][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:27.640][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.641][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:27.643][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.645][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:27.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:27.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:27.649][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:27.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:27.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:27.654][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:27.657][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.658][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:27.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:27.662][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:27.664][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:27.667][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:58:27.669][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:27.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:27.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:27.808][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-30 01:58:27.810][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-30 01:58:27.812][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-30 01:58:27.814][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-30 01:58:27.816][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-30 01:58:27.818][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:58:27.820][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-30 01:58:27.822][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-30 01:58:27.824][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-30 01:58:27.827][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:58:27.829][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:58:27.831][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-30 01:58:27.833][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-30 01:58:27.835][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-30 01:58:27.837][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-30 01:58:27.839][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:58:27.841][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-30 01:58:27.843][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-30 01:58:27.846][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-30 01:58:27.848][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-30 01:58:27.850][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-30 01:58:27.852][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-30 01:58:27.854][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-30 01:58:27.856][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-30 01:58:27.858][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-30 01:58:27.860][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-30 01:58:27.862][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-30 01:58:27.865][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-30 01:58:27.867][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-30 01:58:27.869][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-30 01:58:27.871][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-30 01:58:27.873][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-30 01:58:27.875][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-30 01:58:27.877][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-30 01:58:27.879][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-30 01:58:27.881][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-30 01:58:27.883][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-30 01:58:27.886][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-30 01:58:27.888][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-30 01:58:27.890][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-30 01:58:27.892][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-30 01:58:27.894][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-30 01:58:27.896][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-30 01:58:27.898][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-30 01:58:27.901][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-30 01:58:27.903][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-30 01:58:27.905][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-30 01:58:27.907][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-30 01:58:27.909][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-30 01:58:27.911][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-30 01:58:27.914][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-30 01:58:27.916][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-30 01:58:27.918][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-30 01:58:27.920][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-30 01:58:27.922][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-30 01:58:27.924][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-30 01:58:27.926][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-30 01:58:27.929][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-30 01:58:27.931][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-30 01:58:27.933][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-30 01:58:27.935][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-30 01:58:27.937][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-30 01:58:27.939][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-30 01:58:27.942][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-30 01:58:27.944][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-30 01:58:27.946][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-30 01:58:27.948][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-30 01:58:27.950][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-30 01:58:27.952][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-30 01:58:27.954][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-30 01:58:27.956][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-30 01:58:27.959][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-30 01:58:27.961][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-30 01:58:27.963][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-30 01:58:27.965][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-30 01:58:27.967][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-30 01:58:27.969][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-30 01:58:27.972][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-30 01:58:27.974][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-30 01:58:27.976][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-30 01:58:27.978][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-30 01:58:27.980][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-30 01:58:27.982][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-30 01:58:27.984][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-30 01:58:27.987][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:58:27.988][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:58:27.989][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:27.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:27.992][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.055][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[2023-05-30 01:58:28.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:58:28.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:28.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:28.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:28.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:28.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:28.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:58:28.171][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-30 01:58:28.173][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:58:28.175][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:28.177][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-30 01:58:28.179][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:28.180][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:58:28.182][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:28.183][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:58:28.185][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:28.186][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:58:28.188][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:58:28.189][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:58:28.191][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:28.192][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-30 01:58:28.194][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-30 01:58:28.195][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-30 01:58:28.197][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-30 01:58:28.198][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:58:28.198][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:58:28.200][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:58:28.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:28.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:28.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:58:28.206][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:58:28.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:58:28.209][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:58:28.210][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-30 01:58:28.210][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-30 01:58:28.212][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:58:28.213][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:58:28.215][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-30 01:58:28.216][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:58:28.218][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-30 01:58:28.220][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:58:28.239][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:58:28.241][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-30 01:58:28.243][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-30 01:58:28.245][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-30 01:58:28.247][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-30 01:58:28.249][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-30 01:58:28.251][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-30 01:58:28.252][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-30 01:58:28.254][biodb::testThat]
biodb.INFO [2023-05-30 01:58:28.256][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-05-30 01:58:28.257][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:58:28.258][biodb::testThat]
biodb.DEBUG[2023-05-30 01:58:28.265][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[2023-05-30 01:58:28.270][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-30 01:58:28.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-05-30 01:58:28.274][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:58:28.364][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-05-30 01:58:29.441][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-05-30 01:58:29.443][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-30 01:58:29.445][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-05-30 01:58:29.447][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-05-30 01:58:29.449][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[2023-05-30 01:58:29.451][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:58:29.476][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-30 01:58:29.477][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-30 01:58:29.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:58:29.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:29.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:29.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:29.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:29.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:29.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:58:29.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:29.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:29.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:29.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.534][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:58:29.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:58:29.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.541][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:58:29.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:58:29.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:29.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.553][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:29.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:29.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:29.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:29.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.579][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:58:29.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:29.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.585][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:58:29.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:29.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.595][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:29.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:29.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.601][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:29.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:29.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.627][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:58:29.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-30 01:58:29.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.676][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:58:29.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.734][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.747][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:58:29.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:58:29.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:29.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:29.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:29.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:29.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:29.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:58:29.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:29.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:29.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:29.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:29.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.827][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:58:29.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:58:29.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.833][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:58:29.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:58:29.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.838][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:29.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:29.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.844][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:29.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:29.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.854][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:29.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:29.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:29.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:29.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.869][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:58:29.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:29.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.875][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-30 01:58:29.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:29.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.902][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:29.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:29.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.908][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:29.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:29.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.933][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:58:29.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.938][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-30 01:58:29.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:29.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.956][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-30 01:58:29.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:29.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.965][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.971][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.983][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:29.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:29.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:29.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:29.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:29.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:58:30.043][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-05-30 01:58:30.046][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-30 01:58:30.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:58:30.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:30.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:30.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:30.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:30.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:30.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:58:30.065][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:58:30.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:58:30.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.071][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:58:30.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:58:30.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.077][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-30 01:58:30.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-30 01:58:30.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.083][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-30 01:58:30.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-30 01:58:30.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.088][private$selectFields] Fields none
biodb.TRACE[2023-05-30 01:58:30.090][private$selectFields]
biodb.TRACE[2023-05-30 01:58:30.091][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-05-30 01:58:30.092][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-30 01:58:30.094][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:58:30.095][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.113][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.115][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.117][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.118][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.120][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.123][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.124][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.126][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.127][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.128][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.130][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.131][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.133][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.134][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.136][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.140][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.141][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.143][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.144][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.146][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.148][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.149][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.151][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.152][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.153][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.155][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.158][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.159][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.161][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.162][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.164][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.165][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.168][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.169][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.171][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.172][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.174][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.175][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.177][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.178][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.180][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.181][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.184][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.185][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.187][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.188][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.190][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.191][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.192][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.194][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.195][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.198][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.200][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.201][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.203][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.204][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.205][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:58:30.207][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:58:30.208][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.210][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.211][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.213][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.214][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.216][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.217][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.218][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.220][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.221][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.223][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.224][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.226][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.227][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.229][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.230][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.231][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.233][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.234][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.236][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.237][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.239][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.240][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.241][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.243][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.244][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.246][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.247][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.249][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.250][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.252][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.253][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.255][private$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[2023-05-30 01:58:30.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.298][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.304][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.310][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.338][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.363][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.375][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.399][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.405][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.411][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.425][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-05-30 01:58:30.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:58:30.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:30.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:30.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:30.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:30.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:30.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:58:30.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:58:30.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:58:30.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.450][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:58:30.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:58:30.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.456][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-30 01:58:30.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-30 01:58:30.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.462][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-30 01:58:30.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-30 01:58:30.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.467][private$selectFields] Fields none
biodb.TRACE[2023-05-30 01:58:30.469][private$selectFields]
biodb.TRACE[2023-05-30 01:58:30.470][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-05-30 01:58:30.472][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-30 01:58:30.473][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:58:30.475][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.476][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.478][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.479][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.480][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.482][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.483][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.485][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.486][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.488][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.491][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.492][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.494][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.495][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.496][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.498][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.499][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.501][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.502][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.504][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.505][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.508][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.509][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.514][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.515][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.517][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.518][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.520][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.521][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.523][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.524][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.526][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.527][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.529][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.530][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.548][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.550][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.552][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.554][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.555][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.557][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.558][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.559][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.561][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.562][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.564][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.565][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.567][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.568][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.569][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.571][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.572][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.574][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.575][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.578][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.579][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.581][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.582][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.584][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.585][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:58:30.586][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-30 01:58:30.588][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.589][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.591][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.592][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.593][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.595][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.596][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.598][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.599][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.601][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.602][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.603][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.605][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.606][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.609][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.610][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.615][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.616][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.618][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.619][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.620][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.622][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.623][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.625][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.626][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.627][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.629][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.630][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.632][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.633][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-05-30 01:58:30.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:58:30.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:58:30.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:58:30.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.681][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.690][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.697][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:58:30.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.703][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.709][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.716][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:58:30.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:58:30.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.748][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.755][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:58:30.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:58:30.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:58:30.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:58:30.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.801][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.807][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.813][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-30 01:58:30.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:58:30.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:58:30.824][private$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[2023-05-30 01:58:30.825][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-30 01:58:30.826][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-05-30 01:58:30.830][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-30 01:58:30.832][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-30 01:58:30.834][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-30 01:58:30.835][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-30 01:58:30.836][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:58:30.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:58:30.839][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:58:30.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:58:30.841][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:58:30.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 156 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (???): annotateMzValues() accepts a single vector. ────────────────────
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)
── 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 2 | WARN 0 | SKIP 0 | PASS 156 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn 1.548 0.04410.046
LipidmapsStructureEntry0.2570.0000.257