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This page was generated on 2024-03-29 11:37:32 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 200/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_18
git_last_commit: f02eedd
git_last_commit_date: 2023-10-24 11:38:15 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for biodbLipidmaps on merida1


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

raw results

Summary

Package: biodbLipidmaps
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.8.0.tar.gz
StartedAt: 2024-03-27 23:53:43 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:57:56 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 253.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.8.0’
* 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 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 4.052  1.244   6.387
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 [2024-03-27 23:55:12.386][biodb::testContext]
biodb.INFO [2024-03-27 23:55:12.395][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:55:12.398][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-27 23:55:12.400][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:55:12.403][biodb::testContext]
biodb.INFO [2024-03-27 23:55:12.419][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-27 23:55:12.423][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 23:55:12.441][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:55:12.444][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 23:55:12.446][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 23:55:12.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.458][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 23:55:12.518][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 23:55:12.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.537][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 23:55:12.541][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 23:55:12.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.556][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 23:55:12.560][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 23:55:12.563][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 23:55:12.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.574][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 23:55:12.577][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 23:55:12.580][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 23:55:12.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.591][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 23:55:12.595][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 23:55:12.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.604][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 23:55:12.610][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 23:55:12.613][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 23:55:12.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.629][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 23:55:12.632][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 23:55:12.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.639][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[2024-03-27 23:55:12.643][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 23:55:12.646][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 23:55:12.649][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 23:55:12.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.668][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:55:12.671][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 23:55:12.674][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 23:55:12.677][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 23:55:12.679][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 23:55:12.683][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 23:55:12.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.694][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 23:55:12.696][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 23:55:12.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.707][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 23:55:12.710][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 23:55:12.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.721][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 23:55:12.724][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 23:55:12.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.735][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 23:55:12.738][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 23:55:12.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.751][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 23:55:12.756][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 23:55:12.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.766][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:55:12.769][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 23:55:12.793][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 23:55:12.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.804][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 23:55:12.807][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 23:55:12.810][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 23:55:12.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:12.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:12.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:12.834][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 23:55:12.939][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:12.988][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 23:55:12.992][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:12.995][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:55:12.998][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.002][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.005][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.010][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:55:13.014][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:55:13.018][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.023][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 23:55:13.028][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:55:13.032][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.036][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.040][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:55:13.040][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:55:13.040][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:55:13.040][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:55:13.040][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:55:13.043][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:55:13.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:13.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:13.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:55:13.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:13.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:13.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.062][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:55:13.081][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:55:13.083][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.085][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.088][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 23:55:13.092][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.096][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:55:13.098][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:55:13.103][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.114][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.116][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.118][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:55:13.120][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:55:13.123][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.125][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 23:55:13.127][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:55:13.129][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.158][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.170][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:55:13.170][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:55:13.170][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:55:13.170][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:55:13.170][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:55:13.173][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:55:13.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:13.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:13.182][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:55:13.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:13.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:13.189][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.191][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.193][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:55:13.195][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:55:13.206][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.208][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.211][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 23:55:13.214][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.220][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 23:55:13.225][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.227][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:55:13.231][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.233][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.236][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.238][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.240][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:55:13.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:55:13.254][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.257][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 23:55:13.259][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:55:13.263][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.266][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.268][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.271][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:55:13.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:13.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:13.279][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:55:13.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:13.284][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:13.287][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.291][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:55:13.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:55:13.299][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.301][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.304][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 23:55:13.308][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.311][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:55:13.313][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.315][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:55:13.317][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.319][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.322][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.324][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.326][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:55:13.328][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:55:13.330][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.332][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 23:55:13.334][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:55:13.337][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.339][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:13.342][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.345][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:55:13.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:13.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:13.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:55:13.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:13.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:13.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:55:13.360][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.362][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:55:13.364][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:55:13.368][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:13.371][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:13.381][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:55:13.391][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.477][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[2024-03-27 23:55:13.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.611][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 23:55:13.620][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 23:55:13.624][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 23:55:13.629][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 23:55:13.632][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 23:55:13.635][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 23:55:13.639][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 23:55:13.642][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 23:55:13.645][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 23:55:13.649][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 23:55:13.652][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 23:55:13.655][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 23:55:13.659][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 23:55:13.667][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 23:55:13.674][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 23:55:13.679][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:55:13.683][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 23:55:13.687][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 23:55:13.690][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 23:55:13.694][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 23:55:13.697][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 23:55:13.701][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 23:55:13.704][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 23:55:13.708][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 23:55:13.713][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 23:55:13.717][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 23:55:13.720][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 23:55:13.723][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 23:55:13.726][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 23:55:13.730][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 23:55:13.733][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 23:55:13.737][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 23:55:13.740][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 23:55:13.744][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 23:55:13.747][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 23:55:13.751][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 23:55:13.754][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 23:55:13.763][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 23:55:13.767][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 23:55:13.770][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 23:55:13.777][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 23:55:13.780][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 23:55:13.784][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 23:55:13.787][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 23:55:13.791][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 23:55:13.794][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 23:55:13.797][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 23:55:13.801][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 23:55:13.804][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 23:55:13.808][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 23:55:13.811][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 23:55:13.815][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 23:55:13.819][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 23:55:13.828][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 23:55:13.831][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 23:55:13.834][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 23:55:13.838][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 23:55:13.841][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 23:55:13.844][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 23:55:13.849][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 23:55:13.853][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 23:55:13.857][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 23:55:13.861][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 23:55:13.865][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 23:55:13.870][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 23:55:13.885][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 23:55:13.888][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 23:55:13.891][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 23:55:13.894][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 23:55:13.897][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 23:55:13.900][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 23:55:13.903][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 23:55:13.907][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 23:55:13.910][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 23:55:13.914][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 23:55:13.917][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 23:55:13.921][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 23:55:13.924][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 23:55:13.927][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 23:55:13.931][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 23:55:13.934][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 23:55:13.938][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 23:55:13.943][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 23:55:13.958][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 23:55:13.962][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-27 23:55:13.969][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:55:13.971][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:13.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:13.975][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:13.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:13.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:13.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:13.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:13.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.196][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[2024-03-27 23:55:14.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.303][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[2024-03-27 23:55:14.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:55:14.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:14.327][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 23:55:14.353][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:55:14.363][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:14.367][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 23:55:14.370][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:14.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:55:14.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:14.383][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:55:14.385][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:14.387][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:55:14.390][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:55:14.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:55:14.400][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:14.402][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 23:55:14.404][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 23:55:14.406][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 23:55:14.415][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 23:55:14.417][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:55:14.417][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:55:14.420][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:55:14.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:14.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:14.426][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:55:14.428][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:55:14.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:55:14.432][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:55:14.436][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:55:14.436][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 23:55:14.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:55:14.441][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:55:14.444][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 23:55:14.446][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:55:14.460][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 23:55:14.463][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:55:14.521][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:55:14.524][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 23:55:14.535][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:55:14.544][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 23:55:14.554][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:55:14.556][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:55:14.563][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 23:55:14.565][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 23:55:14.591][biodb::testThat]
biodb.INFO [2024-03-27 23:55:14.595][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-03-27 23:55:14.597][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:14.599][biodb::testThat]
biodb.TRACE[2024-03-27 23:55:14.615][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-03-27 23:55:14.619][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 23:55:14.627][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:55:14.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:14.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:14.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:14.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:14.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:14.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:14.717][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.TRACE[2024-03-27 23:55:14.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:14.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:14.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:55:14.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:55:14.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.830][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:55:14.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:55:14.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.840][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:55:14.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:55:14.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.853][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:14.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:14.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.937][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:14.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:14.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:14.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:14.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:14.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:14.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.976][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:55:14.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:14.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:14.989][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:55:14.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:14.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:14.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.003][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:15.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:15.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:15.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:15.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.054][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:55:15.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.065][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:55:15.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.104][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:55:15.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.326][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.338][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.362][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:15.463][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-27 23:55:15.495][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:55:15.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:55:15.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.513][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:55:15.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:55:15.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.525][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 23:55:15.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 23:55:15.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.539][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 23:55:15.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 23:55:15.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.721][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.750][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:15.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.816][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.820][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.825][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:15.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.890][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.893][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.897][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:15.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:15.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.950][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.958][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.962][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.967][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:15.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:15.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:15.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:16.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:16.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:16.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:16.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.021][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:16.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:16.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.030][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:16.033][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:16.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.037][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.039][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:16.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:16.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.136][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.138][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.142][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.181][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.193][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.202][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.214][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.217][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.223][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.226][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.256][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:16.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:16.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.264][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.274][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:16.277][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:16.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.283][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.295][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:16.297][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:16.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.303][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.327][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.331][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.335][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.350][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.354][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.358][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.376][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.378][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.386][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 23:55:16.404][biodb::testThat]
biodb.INFO [2024-03-27 23:55:16.406][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-27 23:55:16.411][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:16.416][biodb::testThat]
biodb.DEBUG[2024-03-27 23:55:16.453][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-03-27 23:55:16.468][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 23:55:16.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-03-27 23:55:16.483][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:55:16.487][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-03-27 23:55:16.489][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:55:16.557][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 23:55:16.560][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:55:16.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:16.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:16.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:16.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:16.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:16.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:16.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:55:16.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:16.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:16.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:16.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:16.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:55:16.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:55:16.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:55:16.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:55:16.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.672][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:55:16.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:55:16.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.681][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:55:16.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:55:16.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.691][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:16.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.719][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:16.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:16.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.730][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:16.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:16.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.742][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:55:16.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.754][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:55:16.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:16.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:16.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:16.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:16.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:16.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.822][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:55:16.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.831][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:55:16.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.860][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:55:16.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:16.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:16.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:16.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:16.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.938][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:16.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:16.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:16.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:16.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.966][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:16.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:16.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:16.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:16.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:16.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:16.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:16.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:17.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:17.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:17.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:17.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:17.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:17.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:17.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:17.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:17.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:17.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:17.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:17.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:17.053][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-27 23:55:17.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-27 23:55:17.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-27 23:55:17.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:17.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-27 23:55:17.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-27 23:55:17.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:17.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-27 23:55:17.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-27 23:55:17.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:55:17.155][biodb::testThat]
biodb.INFO [2024-03-27 23:55:17.158][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-27 23:55:17.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:17.163][biodb::testThat]
biodb.TRACE[2024-03-27 23:55:17.170][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:17.173][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:17.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.181][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:17.184][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-03-27 23:55:17.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:17.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:17.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:17.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:17.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:17.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:17.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:17.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:17.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:17.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:17.307][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:55:17.322][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:55:17.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:55:17.386][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:55:17.390][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-03-27 23:55:18.490][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-03-27 23:55:19.104][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:55:19.110][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-03-27 23:55:19.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-03-27 23:55:19.186][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-03-27 23:55:19.219][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:19.221][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:19.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:19.226][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 23:55:19.236][biodb::testThat]
biodb.INFO [2024-03-27 23:55:19.240][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-03-27 23:55:19.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:19.245][biodb::testThat]
biodb.TRACE[2024-03-27 23:55:19.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:19.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:19.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:19.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:19.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:19.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:19.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:19.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:19.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:19.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:19.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:19.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:19.711][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:55:19.719][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:55:19.758][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 23:55:19.761][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:55:19.764][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-03-27 23:55:19.803][biodb::testThat]
biodb.INFO [2024-03-27 23:55:19.806][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-03-27 23:55:19.808][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:19.811][biodb::testThat]
biodb.TRACE[2024-03-27 23:55:19.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:55:19.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:55:19.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:19.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:19.907][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:55:19.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:55:19.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:19.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:19.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 23:55:19.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 23:55:19.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:19.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:19.929][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 23:55:19.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 23:55:19.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:19.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:20.044][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:55:20.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:55:20.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:20.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:20.055][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:55:20.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:55:20.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:20.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:20.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 23:55:20.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 23:55:20.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:20.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:20.073][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 23:55:20.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 23:55:20.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:20.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:55:20.097][biodb::testThat]
biodb.INFO [2024-03-27 23:55:20.099][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-27 23:55:20.101][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:20.103][biodb::testThat]
biodb.INFO [2024-03-27 23:55:20.124][biodb::testThat]
biodb.INFO [2024-03-27 23:55:20.127][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-27 23:55:20.130][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:20.132][biodb::testThat]
biodb.INFO [2024-03-27 23:55:20.149][biodb::testThat]
biodb.INFO [2024-03-27 23:55:20.152][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-27 23:55:20.154][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:20.157][biodb::testThat]
biodb.DEBUG[2024-03-27 23:55:20.165][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-03-27 23:55:20.901][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-03-27 23:55:21.317][biodb::testThat]
biodb.INFO [2024-03-27 23:55:21.319][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-27 23:55:21.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:21.323][biodb::testThat]
biodb.TRACE[2024-03-27 23:55:21.336][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:21.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:21.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.407][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:21.410][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:21.412][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:21.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.416][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 23:55:21.420][biodb::testThat]
biodb.INFO [2024-03-27 23:55:21.422][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-03-27 23:55:21.424][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:21.426][biodb::testThat]
biodb.TRACE[2024-03-27 23:55:21.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:21.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:21.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:21.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:21.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:21.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:21.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:21.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:21.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:21.670][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:55:21.678][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:55:21.690][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 23:55:21.694][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:55:21.706][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-03-27 23:55:21.874][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:55:21.895][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:55:21.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 23:55:21.903][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:55:21.906][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-03-27 23:55:21.937][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 23:55:21.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 23:55:21.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:21.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 23:55:21.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 23:55:21.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:21.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:21.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:21.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:21.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:21.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:21.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:21.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:21.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:21.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:21.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:22.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:22.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:22.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:22.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:22.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:22.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:22.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:22.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:22.036][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-03-27 23:55:22.086][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:55:22.129][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:55:22.179][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-03-27 23:55:26.095][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-03-27 23:55:32.040][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-03-27 23:55:32.044][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-03-27 23:55:32.048][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-03-27 23:55:32.200][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-03-27 23:55:34.116][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-03-27 23:55:34.124][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:55:34.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:55:34.133][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-03-27 23:55:34.749][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-03-27 23:55:35.368][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:55:35.372][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-03-27 23:55:35.381][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-03-27 23:55:35.428][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-03-27 23:55:35.436][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:55:35.438][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:55:35.443][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-03-27 23:55:36.099][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-03-27 23:55:36.712][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-03-27 23:55:36.715][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-03-27 23:55:36.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-03-27 23:55:36.727][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-03-27 23:55:36.766][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 23:55:36.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 23:55:36.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:36.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:55:36.792][biodb::testThat]
biodb.INFO [2024-03-27 23:55:36.794][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-27 23:55:36.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:36.798][biodb::testThat]
biodb.TRACE[2024-03-27 23:55:36.804][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 23:55:36.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 23:55:36.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:36.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:36.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 23:55:36.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 23:55:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:36.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:36.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:36.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:36.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:36.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:36.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:36.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:36.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:36.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:36.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:36.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:36.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:36.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:36.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:36.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:36.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:36.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:36.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:36.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:36.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:36.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:36.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:36.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:36.894][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-03-27 23:55:36.902][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:55:36.905][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:55:36.910][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-03-27 23:55:41.181][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-03-27 23:55:47.072][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:55:47.077][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-03-27 23:55:47.210][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-03-27 23:55:49.140][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-03-27 23:55:49.257][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 23:55:49.261][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-03-27 23:55:49.264][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-27 23:55:49.267][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 23:55:49.269][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:55:49.274][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:55:49.277][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 23:55:49.279][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 23:55:49.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:49.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:49.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:49.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:49.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:49.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:49.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:49.350][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-03-27 23:55:49.361][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:55:49.363][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:55:49.366][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:55:49.993][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-03-27 23:55:50.622][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:55:50.627][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-03-27 23:55:50.656][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-03-27 23:55:50.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:50.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:50.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:50.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:50.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:50.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:50.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:55:50.692][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-03-27 23:55:50.699][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:55:50.701][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:55:50.704][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-03-27 23:55:51.331][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-03-27 23:55:51.950][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:55:51.954][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-03-27 23:55:51.961][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-03-27 23:55:51.967][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-03-27 23:55:51.971][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 23:55:51.974][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 23:55:51.977][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:55:51.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:51.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:51.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:51.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:51.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:51.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:52.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:55:52.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:55:52.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:55:52.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:55:52.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:55:52.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.086][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:55:52.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:55:52.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.096][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:55:52.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:55:52.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.107][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:52.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:52.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.116][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:52.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:52.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.125][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:52.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:52.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.135][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:52.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:52.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.145][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:55:52.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:52.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.155][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:55:52.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:52.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:52.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:52.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:52.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:52.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:52.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:52.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.209][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:55:52.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.223][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:55:52.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:52.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:52.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.249][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:55:52.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.270][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.282][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.309][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:52.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:52.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:52.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:52.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:52.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:52.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:52.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:55:52.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:55:52.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:55:52.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.412][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:55:52.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:55:52.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.425][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:55:52.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:55:52.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.435][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:52.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:52.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.446][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:52.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:55:52.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:52.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:52.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:52.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:55:52.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.503][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:55:52.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:52.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.516][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:55:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:52.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:52.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:55:52.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:55:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:52.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:52.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.570][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:55:52.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.581][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:55:52.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:52.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:55:52.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.618][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:55:52.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:55:52.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.629][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.655][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:55:52.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:55:52.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:52.746][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-03-27 23:55:52.770][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 23:55:52.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:52.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:52.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:52.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:52.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:52.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:52.796][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[2024-03-27 23:55:52.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.809][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.819][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:52.821][private$selectFields]
biodb.TRACE[2024-03-27 23:55:52.823][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:55:52.825][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:55:52.828][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:52.830][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.832][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.837][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.840][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.843][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.848][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.850][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:52.853][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:52.855][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.857][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.862][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.864][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:55:52.866][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.875][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.911][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:52.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:52.957][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 23:55:52.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:52.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:52.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:52.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:52.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:52.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:52.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:55:52.993][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:52.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.003][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.015][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:53.018][private$selectFields]
biodb.TRACE[2024-03-27 23:55:53.020][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:55:53.022][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:55:53.025][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:53.029][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.031][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.036][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.039][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.042][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.047][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.049][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:53.052][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:53.054][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.057][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.062][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.065][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:55:53.068][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.081][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.093][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.105][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 23:55:53.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:53.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:53.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:53.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:53.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:53.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:53.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:55:53.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.144][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.156][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:53.159][private$selectFields]
biodb.TRACE[2024-03-27 23:55:53.162][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:55:53.164][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:55:53.167][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:53.169][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.172][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.176][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.179][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.182][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.186][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.188][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:53.190][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:55:53.192][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.195][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.199][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.201][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:55:53.204][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.213][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.222][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:55:53.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.232][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 23:55:53.234][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 23:55:53.236][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 23:55:53.257][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 23:55:53.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 23:55:53.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:55:53.273][biodb::testThat]
biodb.INFO [2024-03-27 23:55:53.275][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-27 23:55:53.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:55:53.279][biodb::testThat]
biodb.TRACE[2024-03-27 23:55:53.285][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 23:55:53.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 23:55:53.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 23:55:53.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 23:55:53.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:53.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:53.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:53.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:53.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:53.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:53.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:55:53.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:53.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:55:53.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:55:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:55:53.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:55:53.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:55:53.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:55:53.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:55:53.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:55:53.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:55:53.528][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[2024-03-27 23:55:53.535][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-03-27 23:55:53.544][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:55:53.546][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:55:53.551][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-03-27 23:55:57.618][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-03-27 23:56:03.519][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:56:03.523][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-03-27 23:56:03.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-03-27 23:56:05.679][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 23:56:05.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:05.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:05.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:05.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:05.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:05.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:05.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:56:05.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:05.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:05.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:05.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:05.875][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:05.877][private$selectFields]
biodb.TRACE[2024-03-27 23:56:05.879][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:56:05.881][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:56:05.883][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:05.886][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.888][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:05.893][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:05.895][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.897][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:05.901][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:05.903][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:05.927][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:05.929][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.931][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:05.936][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:05.939][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:56:05.942][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:05.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:05.979][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:05.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:05.994][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:05.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.012][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 23:56:06.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:06.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:06.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:06.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:06.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:06.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:06.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:56:06.042][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.060][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:06.063][private$selectFields]
biodb.TRACE[2024-03-27 23:56:06.065][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:56:06.067][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:56:06.069][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:06.072][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.074][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.078][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.081][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.083][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.088][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.091][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:06.093][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:06.096][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.098][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.104][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.106][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:56:06.109][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.120][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.130][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.142][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 23:56:06.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:06.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:06.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:06.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:06.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:06.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:06.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:56:06.175][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.186][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.198][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:06.200][private$selectFields]
biodb.TRACE[2024-03-27 23:56:06.202][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:56:06.204][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:56:06.207][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:06.210][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.212][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.218][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.220][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.223][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.227][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.230][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:06.232][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:06.234][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.236][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.243][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.245][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:56:06.247][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.257][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.266][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:06.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.277][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 23:56:06.280][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 23:56:06.282][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 23:56:06.304][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 23:56:06.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 23:56:06.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:56:06.320][biodb::testThat]
biodb.INFO [2024-03-27 23:56:06.322][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-27 23:56:06.324][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:56:06.326][biodb::testThat]
biodb.TRACE[2024-03-27 23:56:06.333][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 23:56:06.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 23:56:06.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 23:56:06.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 23:56:06.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:56:06.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:56:06.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:56:06.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:56:06.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:56:06.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:56:06.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:06.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:56:06.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:56:06.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:06.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:56:06.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:06.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:06.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:06.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:06.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:06.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:06.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:56:06.459][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-03-27 23:56:06.468][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:56:06.471][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-03-27 23:56:06.475][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:56:06.538][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-03-27 23:56:08.864][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 23:56:08.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:08.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:08.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:08.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:08.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:08.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:08.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:56:08.901][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:08.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:08.913][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:08.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:08.924][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:08.928][private$selectFields]
biodb.TRACE[2024-03-27 23:56:08.931][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:56:08.933][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:56:08.937][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:08.939][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.942][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:08.947][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:08.950][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.952][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:08.960][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:08.963][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:08.965][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:08.968][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.972][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:08.976][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:08.978][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:56:08.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:08.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:08.992][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:08.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.005][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.017][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 23:56:09.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:09.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:09.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:09.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:09.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:09.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:09.044][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.TRACE[2024-03-27 23:56:09.047][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.071][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:09.074][private$selectFields]
biodb.TRACE[2024-03-27 23:56:09.076][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:56:09.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:56:09.083][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:09.085][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.088][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.093][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.097][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.100][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.106][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.108][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:09.111][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:09.117][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.119][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.124][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.126][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:56:09.132][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.142][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.155][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.169][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 23:56:09.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:09.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:09.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:09.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:09.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:09.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:09.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:56:09.209][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.223][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.233][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:09.236][private$selectFields]
biodb.TRACE[2024-03-27 23:56:09.239][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:56:09.242][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:56:09.244][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:09.246][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.250][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.256][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.259][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.264][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.271][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.274][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:09.283][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:56:09.285][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.289][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.295][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.297][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:56:09.300][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.311][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.323][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:09.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:09.338][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 23:56:09.346][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 23:56:09.619][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 23:56:09.664][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 23:56:09.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 23:56:09.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:09.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:56:09.679][biodb::testThat]
biodb.INFO [2024-03-27 23:56:09.681][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-03-27 23:56:09.683][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:56:09.685][biodb::testThat]
biodb.DEBUG[2024-03-27 23:56:09.689][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-27 23:56:09.691][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 23:56:09.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-27 23:56:09.697][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 23:56:09.700][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 23:56:09.702][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:56:09.704][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:56:09.706][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 23:56:09.708][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 23:56:09.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:09.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:09.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:09.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:09.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:09.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:09.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:56:09.764][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-03-27 23:56:09.770][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:09.772][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:09.775][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:10.366][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:10.368][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:10.370][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:10.373][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:10.962][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:10.964][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:10.966][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:10.969][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:11.562][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:11.564][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:11.566][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:11.569][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:12.440][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:12.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:12.444][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:12.447][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:13.036][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:13.038][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:13.040][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:13.042][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:13.635][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:13.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:13.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:13.643][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:14.242][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:14.244][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:14.246][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:14.249][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:15.216][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:15.219][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:15.221][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:15.224][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:15.820][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:15.822][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:15.824][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:15.826][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:16.557][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:16.559][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:16.562][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:16.564][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:17.160][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:17.162][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:17.164][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:17.169][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:17.827][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:17.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:17.832][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:17.835][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:18.398][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:18.401][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:18.403][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:18.405][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:19.533][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:19.536][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:19.538][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:19.541][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:20.134][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:20.136][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:20.138][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:20.141][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:20.683][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:20.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:20.687][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:20.690][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:21.243][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:21.245][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:21.247][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:21.263][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:22.180][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:22.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:22.185][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:22.188][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:56:22.737][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:22.739][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:22.742][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:22.744][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:56:23.291][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-27 23:56:23.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-03-27 23:56:23.300][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 23:56:23.303][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 23:56:23.306][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:56:23.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:23.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:23.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:23.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:23.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:23.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:23.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:56:23.337][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:23.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:23.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:23.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:23.347][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:23.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:23.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:23.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:23.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:23.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:23.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:23.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:23.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:23.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:23.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:23.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:23.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:23.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:23.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:23.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:23.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:23.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:23.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:23.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:23.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:23.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:23.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:23.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:23.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:23.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:23.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:23.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:56:23.452][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-03-27 23:56:23.454][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-27 23:56:23.472][biodb::testThat]
biodb.INFO [2024-03-27 23:56:23.475][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-27 23:56:23.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:56:23.479][biodb::testThat]
biodb.DEBUG[2024-03-27 23:56:23.497][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-03-27 23:56:23.500][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-03-27 23:56:23.502][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 23:56:23.506][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-03-27 23:56:23.509][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-27 23:56:23.511][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 23:56:23.513][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:56:23.515][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:56:23.517][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 23:56:23.519][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 23:56:23.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:23.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:23.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:23.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:23.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:23.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:23.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:56:23.550][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-03-27 23:56:23.556][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:23.558][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:23.561][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:24.093][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:24.096][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:24.098][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:24.100][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:24.907][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:24.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:24.911][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:24.914][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:25.463][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:25.465][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:25.468][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:25.470][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:26.191][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:26.193][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:26.195][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:26.198][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:26.744][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:26.746][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:26.748][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:26.751][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:27.294][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:27.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:27.299][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:27.302][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:27.857][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:27.859][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:27.862][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:27.864][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:28.713][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:28.715][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:28.717][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:28.720][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:29.264][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:29.266][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:29.269][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:29.271][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:30.044][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:30.047][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:30.049][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:30.052][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:30.597][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:30.599][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:30.601][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:30.603][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:31.386][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:31.388][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:31.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:31.393][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:31.940][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:31.942][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:31.944][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:31.946][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:32.715][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:32.717][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:32.720][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:32.723][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:33.265][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:33.267][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:33.269][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:33.271][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:33.813][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:33.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:33.818][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:33.820][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:34.372][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:34.375][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:34.377][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:34.379][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:34.926][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:34.929][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:34.931][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:34.933][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:56:35.483][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:35.485][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:35.487][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:35.490][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:56:36.032][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:36.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:36.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:36.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:36.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:36.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:36.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:36.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:56:36.057][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-03-27 23:56:36.063][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:36.065][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:36.068][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:36.616][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:36.618][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:36.620][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:36.623][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:37.164][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:37.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:37.168][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:37.171][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:37.721][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:37.723][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:37.725][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:37.727][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:38.264][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:38.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:38.269][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:38.272][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:38.866][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:38.868][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:38.870][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:38.873][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:39.752][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:39.754][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:39.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:39.759][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:40.308][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:40.310][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:40.312][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:40.315][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:40.868][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:40.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:40.873][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:40.876][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:41.420][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:41.422][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:41.424][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:41.427][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:42.197][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:42.199][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:42.201][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:42.203][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:42.772][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:42.774][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:42.776][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:42.778][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:43.322][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:43.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:43.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:43.329][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:43.876][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:43.878][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:43.881][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:43.883][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:44.432][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:44.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:44.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:44.440][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:44.981][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:44.983][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:44.986][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:44.988][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:45.763][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:45.765][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:45.767][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:45.770][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:46.320][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:46.322][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:46.324][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:46.327][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:47.136][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:56:47.139][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:47.141][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:47.144][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:56:47.690][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:56:47.692][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:56:47.694][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:56:47.696][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:56:48.590][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-27 23:56:48.595][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-03-27 23:56:48.599][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 23:56:48.601][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 23:56:48.604][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:56:48.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:48.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:48.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:48.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:48.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:48.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:48.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:56:48.630][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:48.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:48.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:48.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:48.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:56:48.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:56:48.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:56:48.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:56:48.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:56:48.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:56:48.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:56:48.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:56:48.682][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:48.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:48.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.692][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:48.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:56:48.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:56:48.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:56:48.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:56:48.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:56:48.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:56:48.806][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-03-27 23:56:48.808][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-27 23:56:48.810][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-03-27 23:56:49.176][biodb::testThat]
biodb.INFO [2024-03-27 23:56:49.178][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-03-27 23:56:49.181][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:56:49.183][biodb::testThat]
biodb.INFO [2024-03-27 23:56:49.279][biodb::testThat]
biodb.INFO [2024-03-27 23:56:49.281][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-03-27 23:56:49.283][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:56:49.285][biodb::testThat]
biodb.INFO [2024-03-27 23:56:49.303][biodb::testThat]
biodb.INFO [2024-03-27 23:56:49.305][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-03-27 23:56:49.307][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:56:49.310][biodb::testThat]
biodb.DEBUG[2024-03-27 23:56:49.316][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-27 23:56:49.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:56:49.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:56:49.330][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-03-27 23:56:53.338][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-03-27 23:56:59.250][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:56:59.254][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-03-27 23:56:59.388][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-03-27 23:57:01.297][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:01.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:01.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:01.307][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:01.309][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:01.312][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:01.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:01.318][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 23:57:01.322][biodb::testThat]
biodb.INFO [2024-03-27 23:57:01.324][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-27 23:57:01.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:57:01.331][biodb::testThat]
biodb.ERROR[2024-03-27 23:57:01.367][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-27 23:57:01.404][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-27 23:57:01.436][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 23:57:01.439][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 23:57:01.442][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 23:57:01.443][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 23:57:01.445][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:01.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:01.450][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:01.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:01.454][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 23:57:01.478][biodb::testContext]
biodb.INFO [2024-03-27 23:57:01.480][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:57:01.482][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-03-27 23:57:01.485][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:57:01.487][biodb::testContext]
biodb.INFO [2024-03-27 23:57:01.491][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-27 23:57:01.495][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 23:57:01.503][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:57:01.506][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 23:57:01.508][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 23:57:01.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.516][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 23:57:01.519][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 23:57:01.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.528][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 23:57:01.530][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 23:57:01.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.538][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 23:57:01.541][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 23:57:01.543][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 23:57:01.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.552][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 23:57:01.554][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 23:57:01.556][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 23:57:01.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.588][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 23:57:01.590][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 23:57:01.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.599][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 23:57:01.601][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 23:57:01.603][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 23:57:01.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.612][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 23:57:01.614][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 23:57:01.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.622][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 23:57:01.624][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 23:57:01.626][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 23:57:01.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.634][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:57:01.636][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 23:57:01.638][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 23:57:01.641][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 23:57:01.643][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 23:57:01.645][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 23:57:01.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.654][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 23:57:01.657][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 23:57:01.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.666][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 23:57:01.670][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 23:57:01.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.678][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 23:57:01.681][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 23:57:01.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.688][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 23:57:01.690][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 23:57:01.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.699][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 23:57:01.701][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 23:57:01.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.708][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:57:01.710][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 23:57:01.731][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 23:57:01.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.739][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 23:57:01.742][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 23:57:01.745][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 23:57:01.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:01.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:01.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:01.753][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 23:57:01.756][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.758][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 23:57:01.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:01.769][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.771][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.773][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.776][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.778][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:57:01.780][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:01.783][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.785][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 23:57:01.787][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:01.789][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.791][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.793][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:57:01.793][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:57:01.793][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:57:01.793][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:57:01.793][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:57:01.795][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:01.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:01.800][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:01.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:01.805][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:01.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:01.809][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.811][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.813][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:01.816][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:01.818][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.821][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.823][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 23:57:01.828][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.830][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:57:01.833][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.835][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:01.838][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.841][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.843][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.846][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.848][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:57:01.851][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:01.854][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.856][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 23:57:01.859][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:01.861][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.884][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.886][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:57:01.886][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:57:01.886][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:57:01.886][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:57:01.886][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:57:01.889][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:01.891][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:01.894][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:01.898][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:01.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:01.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:01.904][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.907][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.909][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:01.911][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:01.913][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.915][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.919][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 23:57:01.923][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.925][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 23:57:01.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.930][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:01.933][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.938][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.944][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.946][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:57:01.949][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:01.951][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.954][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 23:57:01.957][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:01.959][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.961][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:01.964][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.966][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:01.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:01.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:01.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:01.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:01.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:01.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:01.982][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.984][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:01.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:01.989][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:01.991][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:01.994][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 23:57:01.999][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.002][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:57:02.004][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.006][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:02.010][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.012][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:02.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:02.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:02.020][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:57:02.023][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:02.025][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:02.028][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 23:57:02.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:02.032][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:02.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.037][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:02.039][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:02.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:02.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:02.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:02.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:02.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:02.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:02.060][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:02.062][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:02.064][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:02.067][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:02.069][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:02.072][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:57:02.074][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.142][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[2024-03-27 23:57:02.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.196][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[2024-03-27 23:57:02.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.282][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 23:57:02.286][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 23:57:02.289][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 23:57:02.293][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 23:57:02.297][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 23:57:02.301][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 23:57:02.305][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 23:57:02.308][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 23:57:02.312][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 23:57:02.316][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 23:57:02.319][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 23:57:02.323][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 23:57:02.326][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 23:57:02.330][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 23:57:02.335][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 23:57:02.338][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:57:02.341][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 23:57:02.345][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 23:57:02.348][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 23:57:02.351][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 23:57:02.356][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 23:57:02.359][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 23:57:02.362][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 23:57:02.365][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 23:57:02.369][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 23:57:02.373][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 23:57:02.376][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 23:57:02.380][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 23:57:02.383][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 23:57:02.387][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 23:57:02.390][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 23:57:02.394][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 23:57:02.397][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 23:57:02.401][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 23:57:02.404][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 23:57:02.407][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 23:57:02.411][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 23:57:02.414][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 23:57:02.417][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 23:57:02.421][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 23:57:02.425][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 23:57:02.429][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 23:57:02.433][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 23:57:02.437][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 23:57:02.442][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 23:57:02.446][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 23:57:02.449][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 23:57:02.456][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 23:57:02.459][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 23:57:02.487][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 23:57:02.490][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 23:57:02.493][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 23:57:02.497][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 23:57:02.501][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 23:57:02.504][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 23:57:02.507][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 23:57:02.510][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 23:57:02.513][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 23:57:02.517][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 23:57:02.520][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 23:57:02.523][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 23:57:02.525][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 23:57:02.530][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 23:57:02.533][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 23:57:02.536][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 23:57:02.540][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 23:57:02.546][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 23:57:02.549][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 23:57:02.552][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 23:57:02.555][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 23:57:02.561][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 23:57:02.565][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 23:57:02.572][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 23:57:02.576][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 23:57:02.579][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 23:57:02.583][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 23:57:02.586][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 23:57:02.590][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 23:57:02.594][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 23:57:02.598][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 23:57:02.601][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 23:57:02.604][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 23:57:02.607][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 23:57:02.611][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 23:57:02.616][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-27 23:57:02.619][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:57:02.621][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.625][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.687][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[2024-03-27 23:57:02.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:02.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:02.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:02.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:02.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:02.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:02.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:02.903][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 23:57:02.906][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:57:02.910][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:02.913][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 23:57:02.915][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:02.921][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.923][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:02.925][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.928][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:02.930][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:57:02.932][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:02.934][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.936][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 23:57:02.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 23:57:02.939][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 23:57:02.942][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:02.943][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:57:02.943][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:57:02.946][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:02.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:02.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:02.952][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:02.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:02.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:02.958][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:02.960][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:57:02.960][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 23:57:02.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:02.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:02.966][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:02.968][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:02.970][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 23:57:02.974][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:57:02.980][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:57:02.982][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 23:57:02.985][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:57:02.989][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 23:57:02.991][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:57:02.993][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:57:02.996][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 23:57:02.999][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 23:57:03.002][biodb::testThat]
biodb.INFO [2024-03-27 23:57:03.004][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-03-27 23:57:03.006][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:57:03.008][biodb::testThat]
biodb.DEBUG[2024-03-27 23:57:03.016][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-03-27 23:57:03.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:03.027][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:03.051][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-03-27 23:57:03.669][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-03-27 23:57:04.325][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:57:04.329][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-03-27 23:57:04.337][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-03-27 23:57:04.357][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-03-27 23:57:04.365][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:04.368][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:04.372][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-03-27 23:57:04.971][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-03-27 23:57:05.565][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:57:05.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-03-27 23:57:05.580][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-03-27 23:57:05.604][biodb::testThat]
biodb.INFO [2024-03-27 23:57:05.607][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-03-27 23:57:05.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:57:05.613][biodb::testThat]
biodb.INFO [2024-03-27 23:57:05.673][biodb::testThat]
biodb.INFO [2024-03-27 23:57:05.675][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-03-27 23:57:05.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:57:05.680][biodb::testThat]
biodb.DEBUG[2024-03-27 23:57:05.687][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-27 23:57:05.694][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:05.697][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:05.700][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-03-27 23:57:06.158][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-03-27 23:57:06.606][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:57:06.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-03-27 23:57:06.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-03-27 23:57:06.631][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-27 23:57:06.638][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:57:06.641][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-03-27 23:57:06.644][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:57:06.647][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-03-27 23:57:06.661][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-03-27 23:57:06.702][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:06.705][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:06.709][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-03-27 23:57:07.164][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-03-27 23:57:07.615][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:57:07.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-03-27 23:57:07.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-03-27 23:57:07.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-03-27 23:57:07.651][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:07.653][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:57:07.655][rule$waitAsNeeded] Wait 0.0522549 second(s).
biodb.TRACE[2024-03-27 23:57:07.712][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-03-27 23:57:08.949][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-03-27 23:57:10.457][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:57:10.461][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-03-27 23:57:10.485][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-03-27 23:57:10.759][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-03-27 23:57:10.768][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:10.770][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:10.775][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-03-27 23:57:11.987][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-03-27 23:57:13.471][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:57:13.475][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-03-27 23:57:13.500][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-03-27 23:57:13.813][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 23:57:13.816][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 23:57:13.819][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 23:57:13.821][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 23:57:13.823][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:13.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:13.827][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:13.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:13.831][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 23:57:13.841][biodb::testContext]
biodb.INFO [2024-03-27 23:57:13.844][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:57:13.846][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-03-27 23:57:13.848][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:57:13.850][biodb::testContext]
biodb.INFO [2024-03-27 23:57:13.855][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-27 23:57:13.859][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 23:57:13.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:57:13.870][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 23:57:13.873][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 23:57:13.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.883][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 23:57:13.886][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 23:57:13.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.897][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 23:57:13.900][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 23:57:13.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.909][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 23:57:13.912][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 23:57:13.914][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 23:57:13.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.924][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 23:57:13.926][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 23:57:13.929][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 23:57:13.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.937][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 23:57:13.939][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 23:57:13.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.947][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 23:57:13.950][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 23:57:13.952][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 23:57:13.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.961][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 23:57:13.963][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 23:57:13.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.972][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 23:57:13.974][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 23:57:13.977][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 23:57:13.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:13.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:13.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:13.986][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:57:13.988][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 23:57:13.990][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 23:57:13.993][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 23:57:13.995][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 23:57:13.998][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 23:57:14.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.006][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 23:57:14.009][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 23:57:14.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.022][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 23:57:14.025][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 23:57:14.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.035][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 23:57:14.038][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 23:57:14.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.046][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 23:57:14.049][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 23:57:14.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.058][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 23:57:14.061][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 23:57:14.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.070][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:57:14.072][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 23:57:14.096][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 23:57:14.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.128][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 23:57:14.130][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 23:57:14.132][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 23:57:14.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.140][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 23:57:14.144][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.147][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 23:57:14.149][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.151][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:14.153][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.156][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.158][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.160][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.163][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:57:14.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:14.167][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.170][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 23:57:14.172][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:14.174][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.177][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.180][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:57:14.180][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:57:14.180][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:57:14.180][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:57:14.180][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:57:14.183][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:14.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:14.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:14.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:14.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:14.196][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:14.198][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.201][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.204][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:14.206][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:14.209][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.212][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.215][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 23:57:14.220][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.223][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:57:14.226][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.228][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:14.231][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.233][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.236][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.238][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.241][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:57:14.243][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:14.246][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.248][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 23:57:14.251][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:14.253][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.258][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:57:14.258][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:57:14.258][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:57:14.258][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:57:14.258][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:57:14.265][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:14.268][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:14.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:14.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:14.294][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:14.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:14.299][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.301][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:14.305][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:14.307][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.310][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.312][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 23:57:14.317][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.319][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 23:57:14.322][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:14.326][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.328][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.331][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.333][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.335][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:57:14.337][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:14.340][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.342][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 23:57:14.344][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:14.346][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.348][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.350][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.352][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:14.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:14.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:14.359][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:14.361][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:14.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:14.365][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.367][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.369][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:14.371][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:14.373][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.375][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.378][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 23:57:14.383][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.385][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:57:14.387][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.390][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:14.392][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.394][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.397][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.399][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.401][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:57:14.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:14.423][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.425][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 23:57:14.427][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:14.429][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.431][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:14.433][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.435][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:14.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:14.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:14.441][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:14.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:14.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:14.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:14.449][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.451][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:14.453][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:14.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:14.456][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:14.459][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:57:14.460][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.616][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 23:57:14.619][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 23:57:14.622][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 23:57:14.625][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 23:57:14.629][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 23:57:14.632][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 23:57:14.653][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 23:57:14.656][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 23:57:14.659][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 23:57:14.663][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 23:57:14.665][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 23:57:14.668][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 23:57:14.671][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 23:57:14.674][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 23:57:14.677][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 23:57:14.680][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:57:14.682][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 23:57:14.684][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 23:57:14.686][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 23:57:14.688][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 23:57:14.691][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 23:57:14.693][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 23:57:14.696][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 23:57:14.699][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 23:57:14.702][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 23:57:14.705][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 23:57:14.708][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 23:57:14.711][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 23:57:14.714][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 23:57:14.717][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 23:57:14.720][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 23:57:14.723][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 23:57:14.727][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 23:57:14.730][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 23:57:14.733][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 23:57:14.736][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 23:57:14.739][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 23:57:14.742][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 23:57:14.745][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 23:57:14.748][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 23:57:14.751][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 23:57:14.754][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 23:57:14.757][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 23:57:14.760][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 23:57:14.763][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 23:57:14.766][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 23:57:14.769][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 23:57:14.772][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 23:57:14.775][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 23:57:14.777][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 23:57:14.780][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 23:57:14.783][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 23:57:14.786][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 23:57:14.789][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 23:57:14.792][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 23:57:14.795][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 23:57:14.798][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 23:57:14.801][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 23:57:14.804][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 23:57:14.807][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 23:57:14.810][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 23:57:14.813][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 23:57:14.816][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 23:57:14.819][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 23:57:14.822][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 23:57:14.825][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 23:57:14.829][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 23:57:14.832][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 23:57:14.835][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 23:57:14.838][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 23:57:14.841][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 23:57:14.844][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 23:57:14.846][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 23:57:14.849][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 23:57:14.853][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 23:57:14.856][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 23:57:14.859][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 23:57:14.863][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 23:57:14.866][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 23:57:14.870][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 23:57:14.893][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 23:57:14.896][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 23:57:14.900][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 23:57:14.903][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 23:57:14.907][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-27 23:57:14.909][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:57:14.911][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.915][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.917][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.DEBUG[2024-03-27 23:57:14.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:14.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:14.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:14.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:14.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:14.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:14.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:14.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:14.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:14.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:14.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:14.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:14.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:14.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:14.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:14.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:14.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:14.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:15.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:15.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.036][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[2024-03-27 23:57:15.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:15.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:15.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:15.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:15.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:15.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:57:15.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.148][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[2024-03-27 23:57:15.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:57:15.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:15.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:15.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:15.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:15.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:15.160][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[2024-03-27 23:57:15.164][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 23:57:15.167][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:57:15.170][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:15.172][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 23:57:15.174][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:15.176][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:57:15.178][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:15.180][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:57:15.182][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:15.184][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:57:15.186][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:57:15.188][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:57:15.190][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:15.192][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 23:57:15.195][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 23:57:15.197][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 23:57:15.199][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 23:57:15.200][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:57:15.200][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:57:15.202][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:57:15.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:15.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:15.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:57:15.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:57:15.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:57:15.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:57:15.217][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:57:15.217][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 23:57:15.219][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:57:15.221][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:57:15.223][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 23:57:15.226][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:57:15.228][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 23:57:15.232][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:57:15.240][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:57:15.242][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 23:57:15.245][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:57:15.248][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 23:57:15.251][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:57:15.253][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:57:15.256][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 23:57:15.258][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 23:57:15.261][biodb::testThat]
biodb.INFO [2024-03-27 23:57:15.263][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-03-27 23:57:15.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:57:15.267][biodb::testThat]
biodb.DEBUG[2024-03-27 23:57:15.275][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-27 23:57:15.284][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:57:15.287][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-03-27 23:57:15.290][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:57:15.336][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-03-27 23:57:17.456][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-03-27 23:57:17.458][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 23:57:17.462][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-03-27 23:57:17.464][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2024-03-27 23:57:17.467][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-03-27 23:57:17.469][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:57:17.472][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:57:17.474][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 23:57:17.476][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 23:57:17.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:57:17.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:17.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:17.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:17.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:17.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:17.502][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[2024-03-27 23:57:17.505][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-03-27 23:57:17.512][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:17.515][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:17.517][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:18.072][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:18.074][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:18.077][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:18.079][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:18.626][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:18.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:18.631][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:18.634][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:19.182][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:19.184][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:19.187][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:19.189][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:20.162][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:20.165][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:20.167][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:20.171][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:20.717][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:20.719][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:20.721][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:20.724][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:21.599][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:21.601][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:21.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:21.606][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:22.157][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:22.160][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:22.163][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:22.165][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:22.700][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:22.703][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:22.706][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:22.709][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:23.259][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:23.261][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:23.263][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:23.265][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:23.811][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:23.813][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:23.815][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:23.818][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:24.370][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:24.373][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:24.376][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:24.379][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:25.510][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:25.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:25.561][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:25.565][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:26.118][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:26.120][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:26.123][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:26.125][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:26.670][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:26.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:26.674][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:26.676][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:27.220][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:27.223][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:27.225][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:27.227][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:28.102][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:28.104][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:28.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:28.113][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:28.661][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:28.671][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:28.673][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:28.675][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:29.389][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:57:29.414][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:57:29.417][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:57:29.420][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:57:29.971][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:57:29.973][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:57:29.975][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:57:29.977][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:57:30.523][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-27 23:57:30.527][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2024-03-27 23:57:30.646][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 23:57:30.649][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 23:57:30.652][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:57:30.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:57:30.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:30.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:30.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:30.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:30.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:30.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:57:30.683][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:30.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:30.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.693][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:30.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:30.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:30.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:30.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:57:30.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:57:30.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:30.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:30.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:30.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:30.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:30.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:57:30.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:30.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:30.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:30.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:57:30.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:57:30.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:57:30.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:57:30.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.839][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:57:30.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:57:30.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.861][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:57:30.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:57:30.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.874][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:30.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:30.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.887][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:30.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.898][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:30.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:30.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.908][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:30.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:30.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.927][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:57:30.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:30.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.942][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:57:30.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:30.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.970][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:57:30.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:57:30.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:57:30.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:57:30.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:30.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:30.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:30.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:30.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:31.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.010][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:57:31.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.024][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:57:31.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:31.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:31.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.078][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:57:31.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.101][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.127][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:57:31.289][self$createEntryFromContent] Accession numbers: NA, LMFA00000002.
biodb.DEBUG[2024-03-27 23:57:31.292][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-27 23:57:31.297][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 23:57:31.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:57:31.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:31.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:31.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:31.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:31.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:31.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:57:31.365][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-03-27 23:57:31.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:57:31.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:31.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:31.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:31.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:31.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:31.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:57:31.436][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:57:31.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:57:31.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.454][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:57:31.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:57:31.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.466][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 23:57:31.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 23:57:31.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.478][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 23:57:31.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 23:57:31.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.488][private$selectFields] Fields none
biodb.TRACE[2024-03-27 23:57:31.491][private$selectFields]
biodb.TRACE[2024-03-27 23:57:31.493][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-27 23:57:31.496][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:57:31.498][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:57:31.500][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.503][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.510][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.533][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.539][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.542][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.546][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.550][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.553][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:31.557][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:31.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.563][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.566][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:31.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:31.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.574][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.576][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:57:31.580][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:57:31.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.586][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.592][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:31.624][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.630][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.632][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.636][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.641][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.643][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.646][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.650][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.653][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.655][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.661][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.664][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.667][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.672][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.675][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:31.677][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:31.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.682][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.778][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:31.780][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:31.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.785][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.787][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:57:31.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:57:31.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.794][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.796][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:31.799][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.803][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.805][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.826][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.831][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.833][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:57:31.835][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:57:31.837][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.843][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.846][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.848][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.852][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.854][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.856][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.860][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.862][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:31.865][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:31.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.870][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.872][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:31.875][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:31.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.879][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.881][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:57:31.883][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:57:31.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.886][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.887][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:31.890][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:31.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.894][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.896][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.898][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:31.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.902][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.906][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-03-27 23:57:31.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:57:31.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:57:31.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:57:31.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.975][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.981][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:57:31.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.988][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:31.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:31.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:31.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:31.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:32.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:32.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.006][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:32.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:57:32.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:32.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:32.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:32.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:32.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:57:32.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.053][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:57:32.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:57:32.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.063][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:57:32.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:57:32.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.072][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:57:32.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:57:32.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:32.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:32.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:32.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:32.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:57:32.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:57:32.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.117][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:32.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:32.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.125][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:32.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:32.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.132][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:57:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:57:32.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:57:32.157][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-03-27 23:57:32.160][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 23:57:32.162][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-03-27 23:57:32.174][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 23:57:32.176][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 23:57:32.178][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 23:57:32.180][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 23:57:32.182][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:57:32.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:57:32.185][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:57:32.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:57:32.191][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:57:32.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]

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

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

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

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

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn4.0521.2446.387
LipidmapsStructureEntry0.7850.0371.014