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This page was generated on 2024-05-04 11:38:54 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for biodbLipidmaps on lconway


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

raw results


Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /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_1.10.0.tar.gz
StartedAt: 2024-05-03 20:25:54 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 20:29:11 -0400 (Fri, 03 May 2024)
EllapsedTime: 197.2 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* 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 ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 2.597  1.391  12.949
* 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 161 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-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
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-05-03 20:27:42.081][biodb::testContext]
biodb.INFO [2024-05-03 20:27:42.087][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:27:42.089][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-03 20:27:42.125][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:27:42.158][biodb::testContext]
biodb.INFO [2024-05-03 20:27:42.208][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:27:42.236][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 20:27:42.291][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:27:42.297][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 20:27:42.299][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 20:27:42.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.338][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 20:27:42.631][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 20:27:42.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.660][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 20:27:42.662][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 20:27:42.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.669][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 20:27:42.670][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 20:27:42.672][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 20:27:42.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.713][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 20:27:42.715][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 20:27:42.717][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 20:27:42.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.725][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 20:27:42.726][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 20:27:42.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.737][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 20:27:42.739][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 20:27:42.741][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 20:27:42.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.746][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 20:27:42.753][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 20:27:42.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.761][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 20:27:42.770][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 20:27:42.772][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 20:27:42.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.779][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:27:42.785][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 20:27:42.787][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 20:27:42.788][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 20:27:42.790][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 20:27:42.791][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 20:27:42.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.806][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 20:27:42.808][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 20:27:42.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.819][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 20:27:42.821][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 20:27:42.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.828][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 20:27:42.837][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 20:27:42.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.843][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 20:27:42.844][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 20:27:42.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.859][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 20:27:42.861][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 20:27:42.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.874][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:27:42.876][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 20:27:42.929][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 20:27:42.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.935][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 20:27:42.937][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 20:27:42.938][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 20:27:42.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:42.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:42.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:42.947][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 20:27:43.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.054][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-03 20:27:43.056][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.058][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:27:43.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.063][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.064][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.066][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:27:43.067][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:27:43.069][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.070][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 20:27:43.072][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:27:43.073][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.075][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.076][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:27:43.076][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:27:43.076][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:27:43.076][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:27:43.076][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:27:43.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:27:43.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.081][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:27:43.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.104][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.106][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.107][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:27:43.108][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:27:43.110][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.118][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.120][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 20:27:43.123][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.125][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:27:43.126][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:27:43.128][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.129][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.130][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.132][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:27:43.143][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:27:43.144][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.145][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 20:27:43.146][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:27:43.147][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.148][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.149][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:27:43.149][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:27:43.149][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:27:43.149][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:27:43.149][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:27:43.150][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:27:43.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.153][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:27:43.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.155][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.157][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.171][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.172][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:27:43.173][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:27:43.174][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.175][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.176][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 20:27:43.177][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.178][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-03 20:27:43.179][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.188][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:27:43.207][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.209][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.211][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.212][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.213][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:27:43.226][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:27:43.232][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.235][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 20:27:43.237][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:27:43.246][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.247][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.248][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.249][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:27:43.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.255][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:27:43.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.257][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.258][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.259][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:27:43.259][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:27:43.260][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.261][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.266][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 20:27:43.267][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.268][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:27:43.269][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.270][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:27:43.270][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.271][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.272][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.274][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.278][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:27:43.279][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:27:43.280][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.281][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 20:27:43.282][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:27:43.283][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.283][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.284][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.285][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:27:43.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.287][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:27:43.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.291][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.293][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:27:43.295][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:27:43.296][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.297][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.317][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:27:43.318][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.437][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 20:27:43.440][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 20:27:43.441][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 20:27:43.443][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 20:27:43.444][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:27:43.446][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 20:27:43.447][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 20:27:43.448][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 20:27:43.450][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 20:27:43.452][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 20:27:43.453][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:27:43.455][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 20:27:43.457][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 20:27:43.458][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 20:27:43.459][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 20:27:43.460][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:27:43.461][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 20:27:43.462][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 20:27:43.463][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:27:43.464][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 20:27:43.467][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 20:27:43.468][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 20:27:43.470][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 20:27:43.472][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 20:27:43.473][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 20:27:43.474][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 20:27:43.475][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 20:27:43.476][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 20:27:43.477][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 20:27:43.479][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 20:27:43.482][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 20:27:43.484][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 20:27:43.485][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 20:27:43.486][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 20:27:43.487][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 20:27:43.488][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 20:27:43.490][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 20:27:43.491][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 20:27:43.492][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 20:27:43.493][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 20:27:43.495][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 20:27:43.499][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 20:27:43.501][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 20:27:43.502][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 20:27:43.503][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 20:27:43.504][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 20:27:43.506][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 20:27:43.507][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 20:27:43.515][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 20:27:43.517][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 20:27:43.518][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 20:27:43.520][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 20:27:43.521][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 20:27:43.522][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 20:27:43.524][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 20:27:43.526][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 20:27:43.527][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 20:27:43.528][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 20:27:43.529][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 20:27:43.530][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 20:27:43.532][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 20:27:43.533][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 20:27:43.534][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 20:27:43.535][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 20:27:43.536][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 20:27:43.539][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 20:27:43.540][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:27:43.542][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:27:43.544][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 20:27:43.545][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 20:27:43.547][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 20:27:43.548][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 20:27:43.549][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 20:27:43.550][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 20:27:43.552][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 20:27:43.554][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 20:27:43.556][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 20:27:43.558][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 20:27:43.560][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 20:27:43.561][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 20:27:43.562][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 20:27:43.564][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 20:27:43.565][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 20:27:43.574][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 20:27:43.577][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:27:43.581][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:27:43.582][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.584][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.585][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[2024-05-03 20:27:43.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.608][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[2024-05-03 20:27:43.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.687][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[2024-05-03 20:27:43.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:27:43.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:43.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:43.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:43.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:43.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:43.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:43.737][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-03 20:27:43.747][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:27:43.750][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.752][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.762][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:27:43.763][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.765][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.766][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.767][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.768][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:27:43.769][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:27:43.770][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.770][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-03 20:27:43.771][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-03 20:27:43.773][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-03 20:27:43.776][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 20:27:43.777][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:27:43.777][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:27:43.777][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:27:43.778][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.780][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:27:43.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:27:43.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:27:43.782][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:27:43.783][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-03 20:27:43.783][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-03 20:27:43.784][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:27:43.784][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:27:43.786][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 20:27:43.787][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:27:43.793][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-03 20:27:43.795][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:27:43.857][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:27:43.859][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-03 20:27:43.863][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:27:43.867][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-03 20:27:43.872][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-03 20:27:43.873][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-03 20:27:43.875][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-03 20:27:43.875][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-03 20:27:43.886][biodb::testThat]
biodb.INFO [2024-05-03 20:27:43.887][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-03 20:27:43.889][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:43.890][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:43.961][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-05-03 20:27:43.973][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:27:43.989][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-03 20:27:44.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:44.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:44.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:44.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:44.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:44.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:44.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:44.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:44.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:44.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.315][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:27:44.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:27:44.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.321][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:44.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:44.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.329][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:44.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:44.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.395][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:44.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:44.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.401][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:44.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:44.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.408][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:44.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:44.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.432][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:27:44.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:44.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.440][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:27:44.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:44.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.446][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:44.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:44.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:44.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:44.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.472][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:27:44.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.478][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-03 20:27:44.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.491][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:27:44.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:44.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:44.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.660][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.670][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:44.766][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-03 20:27:44.770][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:27:44.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:27:44.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.774][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:27:44.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:27:44.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 20:27:44.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 20:27:44.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 20:27:44.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 20:27:44.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.872][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.946][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.952][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.956][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:44.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.991][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.993][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:44.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:44.996][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:44.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:44.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.035][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.037][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.040][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.060][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.086][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.095][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.101][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.103][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.105][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.106][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.121][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:45.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:45.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.126][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:45.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:45.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.132][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:45.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:45.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.136][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:45.137][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:45.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.138][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.139][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:45.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:45.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.185][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.186][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.199][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.217][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.223][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.229][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.235][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.236][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.239][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.241][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.281][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.283][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.284][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.293][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.294][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.308][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.314][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:45.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:45.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.318][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.334][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.336][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.339][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.345][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.346][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.347][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.355][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.356][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.358][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:45.370][biodb::testThat]
biodb.INFO [2024-05-03 20:27:45.371][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-03 20:27:45.372][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:45.374][biodb::testThat]
biodb.DEBUG[2024-05-03 20:27:45.392][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-05-03 20:27:45.420][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:27:45.481][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-05-03 20:27:45.493][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:45.495][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-05-03 20:27:45.497][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:45.522][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:27:45.523][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-03 20:27:45.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:45.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:45.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:45.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:45.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:45.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:45.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:45.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:45.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:45.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:45.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:45.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.581][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:27:45.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:27:45.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.586][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:45.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:45.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.592][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.596][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:45.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:45.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.622][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:27:45.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.627][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:27:45.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.631][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:45.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:45.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:45.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:45.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.650][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:27:45.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.656][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-03 20:27:45.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.667][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:27:45.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.699][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:45.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:45.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.710][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:45.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:45.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:45.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:45.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:45.742][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-03 20:27:45.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-03 20:27:45.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-03 20:27:45.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-03 20:27:45.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-03 20:27:45.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-03 20:27:45.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-03 20:27:45.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:45.765][biodb::testThat]
biodb.INFO [2024-05-03 20:27:45.766][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-03 20:27:45.767][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:45.768][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:45.771][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.772][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.775][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:45.777][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-05-03 20:27:45.805][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:45.820][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-03 20:27:45.826][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-03 20:27:45.865][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:45.884][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-03 20:27:45.885][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:45.888][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-03 20:27:45.890][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-05-03 20:27:45.909][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.910][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:45.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.912][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:45.917][biodb::testThat]
biodb.INFO [2024-05-03 20:27:45.918][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-03 20:27:45.919][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:45.920][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:45.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:45.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:45.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:45.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:45.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:46.173][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-03 20:27:46.177][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:46.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-03 20:27:46.179][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:46.181][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-05-03 20:27:46.207][biodb::testThat]
biodb.INFO [2024-05-03 20:27:46.208][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-03 20:27:46.209][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:46.210][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:46.234][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:27:46.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:27:46.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:46.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:46.238][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:27:46.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:27:46.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:46.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:46.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 20:27:46.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 20:27:46.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:46.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:46.256][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 20:27:46.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 20:27:46.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:46.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:46.335][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:27:46.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:27:46.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:46.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:46.340][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:27:46.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:27:46.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:46.344][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 20:27:46.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 20:27:46.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:46.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:46.348][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 20:27:46.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 20:27:46.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:46.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:46.365][biodb::testThat]
biodb.INFO [2024-05-03 20:27:46.367][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-03 20:27:46.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:46.369][biodb::testThat]
biodb.INFO [2024-05-03 20:27:46.379][biodb::testThat]
biodb.INFO [2024-05-03 20:27:46.380][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-03 20:27:46.381][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:46.382][biodb::testThat]
biodb.INFO [2024-05-03 20:27:46.391][biodb::testThat]
biodb.INFO [2024-05-03 20:27:46.403][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-03 20:27:46.404][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:46.405][biodb::testThat]
biodb.DEBUG[2024-05-03 20:27:46.409][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-05-03 20:27:48.303][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-05-03 20:27:49.087][biodb::testThat]
biodb.INFO [2024-05-03 20:27:49.089][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-03 20:27:49.091][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:49.092][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:49.103][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:49.106][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:49.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.109][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.110][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.126][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.132][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:49.135][biodb::testThat]
biodb.INFO [2024-05-03 20:27:49.137][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-03 20:27:49.139][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:49.140][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:49.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:49.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:49.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:49.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:49.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.181][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:49.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:49.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:49.391][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-03 20:27:49.396][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:49.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-03 20:27:49.400][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:49.402][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-03 20:27:49.509][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-03 20:27:49.513][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:49.526][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-03 20:27:49.527][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:49.530][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-05-03 20:27:49.552][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 20:27:49.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 20:27:49.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:49.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:49.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:49.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:49.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:49.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:49.627][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-03 20:27:49.631][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:49.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359".
biodb.TRACE[2024-05-03 20:27:49.634][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:50.262][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content".
biodb.DEBUG[2024-05-03 20:27:53.502][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-03 20:27:53.506][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:53.508][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3".
biodb.TRACE[2024-05-03 20:27:53.509][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:53.511][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content".
biodb.DEBUG[2024-05-03 20:27:53.548][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-05-03 20:27:53.555][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:53.557][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54".
biodb.TRACE[2024-05-03 20:27:53.569][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:53.572][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content".
biodb.TRACE[2024-05-03 20:27:53.593][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:53.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:53.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:53.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:53.607][biodb::testThat]
biodb.INFO [2024-05-03 20:27:53.608][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-03 20:27:53.609][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:53.611][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:53.615][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 20:27:53.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 20:27:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:53.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:53.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:53.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:53.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:53.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:53.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:53.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:53.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:53.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:53.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:53.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:53.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:53.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:53.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:53.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:53.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:53.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:53.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:53.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:53.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:53.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:53.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:53.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:53.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:53.671][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-03 20:27:53.674][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:53.675][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-03 20:27:53.676][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:53.717][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-03 20:27:55.312][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-05-03 20:27:55.374][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-03 20:27:55.376][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-05-03 20:27:55.378][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-03 20:27:55.381][loadFileContents] Loaded 2 files from 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[2024-05-03 20:27:55.382][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:55.383][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-03 20:27:55.384][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-03 20:27:55.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:55.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:55.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:55.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:55.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:55.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:55.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:55.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:55.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:55.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:55.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:55.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:55.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:55.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:55.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:55.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.426][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:27:55.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:27:55.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.431][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:55.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:55.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.435][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:55.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:55.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.438][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:55.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:55.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:55.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:55.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:55.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:55.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.452][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:27:55.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:55.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.480][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:27:55.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:55.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:55.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:55.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:55.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:55.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.507][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:55.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:55.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:55.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:55.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.555][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:27:55.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.604][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-03 20:27:55.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:55.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:55.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:55.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:55.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:55.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.741][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:27:55.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:55.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.747][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:55.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:55.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:55.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:55.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:55.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:55.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.787][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:55.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:55.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:55.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:55.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:55.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:55.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:55.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:55.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:55.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:55.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:55.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:55.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:55.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:55.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:55.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:55.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:55.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:55.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:55.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:55.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:55.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:55.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.953][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:27:55.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:27:55.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.971][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:55.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:55.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:55.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:55.990][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:56.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:56.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.008][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:56.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:27:56.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:56.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:56.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.034][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:56.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:27:56.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.052][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:27:56.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.071][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:27:56.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:56.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:56.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.096][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:56.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:56.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:56.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:56.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:56.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:56.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.118][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:27:56.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:56.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.125][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-03 20:27:56.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:56.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:56.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:56.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:56.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:56.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.145][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:27:56.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:56.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.152][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.158][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.195][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:56.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:56.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:56.249][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-05-03 20:27:56.261][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:27:56.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:56.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:56.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:56.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:56.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:56.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:56.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:56.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.288][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.297][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.299][private$selectFields]
biodb.TRACE[2024-05-03 20:27:56.301][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:56.303][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:56.305][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.307][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.309][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.313][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.318][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.320][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.323][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.325][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.327][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.328][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.330][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.333][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:27:56.334][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.339][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.361][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-03 20:27:56.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:56.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:56.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:56.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:56.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:56.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:56.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:56.379][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.384][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.388][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.389][private$selectFields]
biodb.TRACE[2024-05-03 20:27:56.389][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:56.391][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:56.392][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.392][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.393][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.395][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.396][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.398][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.400][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.402][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.403][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.404][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.406][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.408][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.409][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:27:56.411][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.417][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.422][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.428][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-03 20:27:56.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:56.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:56.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:56.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:56.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:56.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:56.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:56.442][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.447][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.451][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.452][private$selectFields]
biodb.TRACE[2024-05-03 20:27:56.453][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:56.454][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:56.455][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.457][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.458][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.460][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.462][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.463][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.465][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.466][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.468][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:56.469][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.470][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.473][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.474][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:27:56.475][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.485][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:56.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.490][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-03 20:27:56.491][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:27:56.492][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:27:56.504][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:56.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:56.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:56.515][biodb::testThat]
biodb.INFO [2024-05-03 20:27:56.516][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-03 20:27:56.518][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:56.519][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:56.522][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 20:27:56.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 20:27:56.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:56.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:56.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:56.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:56.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:56.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:56.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:56.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:56.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:56.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:56.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:56.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:56.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:56.670][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-05-03 20:27:56.674][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:56.675][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5652f5994fce967a05a065a71bac3ed6".
biodb.TRACE[2024-05-03 20:27:56.677][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:56.723][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content".
biodb.DEBUG[2024-05-03 20:27:58.154][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:27:58.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:58.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:58.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:58.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:58.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:58.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:58.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:58.210][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.213][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.243][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.244][private$selectFields]
biodb.TRACE[2024-05-03 20:27:58.245][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:58.246][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:58.247][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.248][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.249][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.250][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.251][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.252][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.254][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.255][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.263][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.263][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.264][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.266][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.267][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:27:58.269][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.273][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.276][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.291][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-03 20:27:58.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:58.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:58.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:58.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:58.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:58.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:58.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:58.302][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.306][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.311][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.312][private$selectFields]
biodb.TRACE[2024-05-03 20:27:58.313][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:58.315][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:58.317][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.318][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.319][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.321][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.323][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.325][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.327][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.329][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.330][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.331][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.332][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.334][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.335][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:27:58.336][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.341][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.346][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.353][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-03 20:27:58.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:58.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:58.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:58.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:58.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:58.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:58.369][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[2024-05-03 20:27:58.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.378][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.384][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.385][private$selectFields]
biodb.TRACE[2024-05-03 20:27:58.387][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:58.388][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:58.390][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.391][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.393][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.396][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.397][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.398][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.403][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.404][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:27:58.406][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.407][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.410][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.412][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:27:58.413][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.420][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.426][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:27:58.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.432][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-03 20:27:58.434][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:27:58.435][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:27:58.449][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:58.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:58.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:58.462][biodb::testThat]
biodb.INFO [2024-05-03 20:27:58.463][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-03 20:27:58.465][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:58.467][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:58.472][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 20:27:58.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 20:27:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:58.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:58.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:58.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:58.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:58.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:58.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:58.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:58.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:58.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:58.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:58.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:58.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:58.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:58.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:58.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:58.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:58.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:58.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:58.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:58.558][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-03 20:27:58.562][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:58.564][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-03 20:27:58.566][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:58.615][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-03 20:28:00.051][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:28:00.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:00.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:00.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:00.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:00.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:00.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:00.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:00.082][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.102][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.103][private$selectFields]
biodb.TRACE[2024-05-03 20:28:00.105][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:28:00.106][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:28:00.108][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.109][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.140][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.143][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.144][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.145][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.147][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.149][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.151][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.152][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.154][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.157][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.158][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:28:00.160][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.166][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.170][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.175][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-03 20:28:00.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:00.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:00.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:00.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:00.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:00.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:00.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:00.194][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.199][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.202][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.203][private$selectFields]
biodb.TRACE[2024-05-03 20:28:00.204][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:28:00.205][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:28:00.206][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.207][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.210][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.215][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.216][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.218][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.222][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.224][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.225][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.226][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.227][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.230][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.235][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:28:00.237][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.243][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.257][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.266][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-03 20:28:00.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:00.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:00.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:00.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:00.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:00.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:00.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:00.283][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.289][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.295][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.296][private$selectFields]
biodb.TRACE[2024-05-03 20:28:00.297][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:28:00.299][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:28:00.300][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.301][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.303][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.312][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.314][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.316][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.318][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.320][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.321][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:00.326][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.328][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.334][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-03 20:28:00.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.351][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.373][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.382][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-03 20:28:00.383][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:28:00.384][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:28:00.442][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 20:28:00.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 20:28:00.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:28:00.473][biodb::testThat]
biodb.INFO [2024-05-03 20:28:00.480][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-03 20:28:00.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:00.495][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:00.498][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-03 20:28:00.500][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:28:00.515][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-03 20:28:00.522][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:00.526][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv".
biodb.DEBUG[2024-05-03 20:28:00.528][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:28:00.530][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:28:00.533][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-03 20:28:00.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:00.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:00.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:00.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:00.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:00.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:00.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:00.595][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.602][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:00.696][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-03 20:28:00.697][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-03 20:28:00.710][biodb::testThat]
biodb.INFO [2024-05-03 20:28:00.711][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-03 20:28:00.713][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:00.714][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:00.745][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-05-03 20:28:00.747][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-05-03 20:28:00.748][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-03 20:28:00.772][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-05-03 20:28:00.775][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-03 20:28:00.780][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2024-05-03 20:28:00.784][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:28:00.786][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-03 20:28:00.788][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-03 20:28:00.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:00.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:00.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:00.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:00.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:00.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:00.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:00.808][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.824][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:00.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:00.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:00.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:00.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:00.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:00.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:00.943][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.TRACE[2024-05-03 20:28:00.946][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.953][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:00.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:00.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:00.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:00.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:00.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:01.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:01.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:01.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:01.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:01.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:01.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:01.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:01.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:01.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:01.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:01.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:01.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:01.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:01.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:01.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:01.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:01.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:01.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:01.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:01.071][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-03 20:28:01.072][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-03 20:28:01.073][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-05-03 20:28:02.167][biodb::testThat]
biodb.INFO [2024-05-03 20:28:02.168][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-03 20:28:02.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:02.170][biodb::testThat]
biodb.INFO [2024-05-03 20:28:02.303][biodb::testThat]
biodb.INFO [2024-05-03 20:28:02.304][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-03 20:28:02.305][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:02.305][biodb::testThat]
biodb.INFO [2024-05-03 20:28:02.339][biodb::testThat]
biodb.INFO [2024-05-03 20:28:02.340][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-03 20:28:02.340][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:02.341][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:02.344][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-03 20:28:02.370][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:02.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-03 20:28:02.408][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:02.451][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2024-05-03 20:28:05.975][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:05.979][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:05.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:05.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:05.986][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:05.987][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:05.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:05.998][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 20:28:06.006][biodb::testThat]
biodb.INFO [2024-05-03 20:28:06.008][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-03 20:28:06.009][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:06.011][biodb::testThat]
biodb.ERROR[2024-05-03 20:28:06.052][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-03 20:28:06.083][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-03 20:28:06.101][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 20:28:06.103][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-03 20:28:06.105][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-03 20:28:06.106][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 20:28:06.107][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.110][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.112][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 20:28:06.130][biodb::testContext]
biodb.INFO [2024-05-03 20:28:06.132][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:06.133][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-05-03 20:28:06.134][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:06.135][biodb::testContext]
biodb.INFO [2024-05-03 20:28:06.137][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:06.139][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:06.146][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:06.147][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 20:28:06.149][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 20:28:06.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.152][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 20:28:06.153][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 20:28:06.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.163][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 20:28:06.167][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 20:28:06.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.172][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 20:28:06.174][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 20:28:06.175][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 20:28:06.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.178][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 20:28:06.179][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 20:28:06.180][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 20:28:06.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.184][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 20:28:06.229][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 20:28:06.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.234][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 20:28:06.236][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 20:28:06.239][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 20:28:06.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.243][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 20:28:06.244][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 20:28:06.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.248][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 20:28:06.257][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 20:28:06.258][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 20:28:06.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.261][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:06.262][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 20:28:06.263][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 20:28:06.264][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 20:28:06.265][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 20:28:06.270][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 20:28:06.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.276][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 20:28:06.277][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 20:28:06.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.282][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 20:28:06.283][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 20:28:06.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.286][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 20:28:06.287][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 20:28:06.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.293][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 20:28:06.294][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 20:28:06.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.298][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 20:28:06.299][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 20:28:06.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.302][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:06.303][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 20:28:06.389][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 20:28:06.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.394][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 20:28:06.395][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 20:28:06.396][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 20:28:06.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.399][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 20:28:06.402][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.403][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-03 20:28:06.427][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.429][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:06.430][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.431][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.432][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.433][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.433][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:06.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:06.435][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.436][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 20:28:06.437][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:06.437][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.439][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:06.439][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:06.439][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:06.439][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:06.439][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:06.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:06.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:06.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:06.443][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:06.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:06.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:06.445][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.446][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.447][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:06.448][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:06.449][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.450][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.451][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 20:28:06.474][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.476][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:06.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.479][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:06.480][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.481][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.481][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.482][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.483][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:06.484][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:06.485][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.486][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 20:28:06.488][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:06.502][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.504][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.504][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:06.504][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:06.504][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:06.504][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:06.504][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:06.505][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:06.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:06.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:06.508][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:06.510][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:06.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:06.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.523][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.525][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:06.528][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:06.529][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.530][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.531][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 20:28:06.532][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.533][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-03 20:28:06.534][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.535][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:06.536][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.551][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.553][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.554][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.576][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:06.577][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:06.578][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.579][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 20:28:06.594][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:06.595][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.596][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.597][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.598][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:06.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:06.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:06.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:06.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:06.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:06.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.604][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:06.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:06.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.607][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.608][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 20:28:06.610][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.611][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:06.612][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.613][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:06.613][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.614][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.615][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.617][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:06.617][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:06.618][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.619][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 20:28:06.620][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:06.621][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.621][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:06.623][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.624][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:06.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:06.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:06.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:06.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:06.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:06.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:06.629][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.630][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:06.631][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:06.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:06.632][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:06.634][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:06.635][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.643][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[2024-05-03 20:28:06.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.689][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[2024-05-03 20:28:06.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.706][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[2024-05-03 20:28:06.718][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 20:28:06.720][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 20:28:06.721][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 20:28:06.722][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 20:28:06.723][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:28:06.724][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 20:28:06.725][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:06.726][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:06.727][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 20:28:06.728][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 20:28:06.729][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:28:06.730][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 20:28:06.731][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:06.732][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:06.734][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 20:28:06.735][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:28:06.736][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 20:28:06.737][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 20:28:06.738][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:28:06.739][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 20:28:06.740][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 20:28:06.752][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 20:28:06.753][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 20:28:06.754][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 20:28:06.755][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 20:28:06.756][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 20:28:06.757][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 20:28:06.758][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 20:28:06.759][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 20:28:06.760][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 20:28:06.761][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 20:28:06.763][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 20:28:06.764][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 20:28:06.765][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 20:28:06.766][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 20:28:06.767][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 20:28:06.768][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 20:28:06.769][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 20:28:06.770][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 20:28:06.771][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 20:28:06.772][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 20:28:06.773][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 20:28:06.774][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 20:28:06.776][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 20:28:06.777][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 20:28:06.778][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 20:28:06.779][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 20:28:06.780][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 20:28:06.781][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 20:28:06.782][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 20:28:06.784][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 20:28:06.785][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 20:28:06.786][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 20:28:06.787][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 20:28:06.788][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 20:28:06.790][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 20:28:06.791][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 20:28:06.792][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 20:28:06.793][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 20:28:06.794][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 20:28:06.798][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 20:28:06.799][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 20:28:06.800][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 20:28:06.801][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 20:28:06.803][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 20:28:06.804][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 20:28:06.805][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:28:06.806][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:28:06.810][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 20:28:06.811][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 20:28:06.812][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 20:28:06.813][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 20:28:06.815][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 20:28:06.816][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 20:28:06.817][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 20:28:06.818][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 20:28:06.819][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 20:28:06.823][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 20:28:06.825][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 20:28:06.827][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 20:28:06.829][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 20:28:06.830][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 20:28:06.832][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 20:28:06.833][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 20:28:06.844][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:06.846][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:06.847][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.850][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:06.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:06.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:06.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:06.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:06.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:06.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:06.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:07.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:07.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:07.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:07.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:07.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:07.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:07.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:07.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:07.008][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:07.010][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:28:07.011][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:07.013][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 20:28:07.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:07.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:07.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:07.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:07.017][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:07.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:07.019][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:07.020][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:07.021][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:07.022][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-03 20:28:07.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-03 20:28:07.023][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-03 20:28:07.024][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:07.025][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:07.025][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:07.026][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:07.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:07.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:07.028][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:07.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:07.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:07.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:07.032][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-03 20:28:07.032][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-03 20:28:07.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:07.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:07.035][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:07.036][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:07.037][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-03 20:28:07.038][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:28:07.041][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:28:07.043][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-03 20:28:07.044][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:28:07.045][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-03 20:28:07.046][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-03 20:28:07.047][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-03 20:28:07.048][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-03 20:28:07.049][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-03 20:28:07.050][biodb::testThat]
biodb.INFO [2024-05-03 20:28:07.051][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-05-03 20:28:07.052][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:07.052][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:07.056][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-05-03 20:28:07.063][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:07.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cfd52aa1c2e3525a5defd7b7e8bd8bb8".
biodb.TRACE[2024-05-03 20:28:07.066][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:07.071][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content".
biodb.DEBUG[2024-05-03 20:28:07.083][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-05-03 20:28:07.086][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:07.088][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2024-05-03 20:28:07.089][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:07.105][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2024-05-03 20:28:07.122][biodb::testThat]
biodb.INFO [2024-05-03 20:28:07.123][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-05-03 20:28:07.124][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:07.126][biodb::testThat]
biodb.INFO [2024-05-03 20:28:07.160][biodb::testThat]
biodb.INFO [2024-05-03 20:28:07.162][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-05-03 20:28:07.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:07.163][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:07.166][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-03 20:28:07.170][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:07.171][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-03 20:28:07.172][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:07.174][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-03 20:28:07.182][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-03 20:28:07.185][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:07.188][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-03 20:28:07.193][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:07.195][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-03 20:28:07.200][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-05-03 20:28:07.205][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:07.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9edcc233717c530cf0cbf5f73b9c3fc7".
biodb.TRACE[2024-05-03 20:28:07.221][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:07.223][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content".
biodb.DEBUG[2024-05-03 20:28:07.230][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-05-03 20:28:07.235][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:07.236][cch$loadFileContent] Trying to load 1 files from cache: [1]: "be9130a77f849b73da505cd10830451e".
biodb.TRACE[2024-05-03 20:28:07.239][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:07.252][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content".
biodb.DEBUG[2024-05-03 20:28:07.556][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-05-03 20:28:07.564][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:07.566][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971".
biodb.TRACE[2024-05-03 20:28:07.568][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:07.580][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content".
biodb.INFO [2024-05-03 20:28:07.973][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 20:28:07.974][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-03 20:28:07.976][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-03 20:28:07.977][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 20:28:07.977][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:07.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:07.979][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:07.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:07.981][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:07.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 20:28:07.990][biodb::testContext]
biodb.INFO [2024-05-03 20:28:07.992][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:07.994][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-05-03 20:28:07.995][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:07.997][biodb::testContext]
biodb.INFO [2024-05-03 20:28:08.000][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:08.004][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:08.011][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:08.015][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 20:28:08.017][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 20:28:08.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.021][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 20:28:08.022][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 20:28:08.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.026][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 20:28:08.027][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 20:28:08.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.031][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 20:28:08.032][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 20:28:08.033][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 20:28:08.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.035][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[2024-05-03 20:28:08.036][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 20:28:08.037][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 20:28:08.041][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 20:28:08.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.047][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 20:28:08.049][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 20:28:08.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.053][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 20:28:08.055][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 20:28:08.056][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 20:28:08.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.059][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 20:28:08.060][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 20:28:08.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.063][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 20:28:08.064][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 20:28:08.065][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 20:28:08.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.069][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:08.071][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 20:28:08.072][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 20:28:08.073][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 20:28:08.074][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 20:28:08.075][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 20:28:08.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.079][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 20:28:08.081][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 20:28:08.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.087][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 20:28:08.088][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 20:28:08.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.093][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 20:28:08.095][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 20:28:08.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.101][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 20:28:08.102][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 20:28:08.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.107][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 20:28:08.108][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 20:28:08.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.113][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:08.115][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 20:28:08.263][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 20:28:08.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.270][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 20:28:08.271][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 20:28:08.275][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 20:28:08.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.281][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 20:28:08.283][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.285][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-03 20:28:08.286][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:08.289][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.291][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.292][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.295][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:08.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:08.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.306][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 20:28:08.307][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:08.309][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.310][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.312][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:08.312][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:08.312][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:08.312][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:08.312][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:08.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:08.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:08.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:08.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:08.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:08.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:08.325][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.329][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.331][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:08.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:08.334][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.336][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.338][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 20:28:08.358][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.362][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:08.363][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.365][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:08.367][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.378][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.380][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.381][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.383][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:08.384][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:08.386][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.390][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 20:28:08.391][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:08.393][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.395][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.396][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:08.396][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:08.396][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:08.396][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:08.396][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:08.397][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:08.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:08.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:08.420][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:08.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:08.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:08.426][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.429][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.431][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:08.433][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:08.434][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.436][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.438][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 20:28:08.450][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.458][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-03 20:28:08.459][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:08.463][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.473][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.475][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.476][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:08.477][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:08.479][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.480][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 20:28:08.486][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:08.488][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.489][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.491][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.492][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:08.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:08.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:08.497][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:08.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:08.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:08.507][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.509][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.510][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:08.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:08.523][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.525][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.527][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 20:28:08.530][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.544][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:08.546][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.548][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:08.550][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.551][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.553][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.561][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.563][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:08.564][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:08.566][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.567][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 20:28:08.568][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:08.570][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.629][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:08.631][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.633][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:08.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:08.636][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:08.641][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:08.644][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:08.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:08.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:08.649][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.650][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:08.664][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:08.666][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:08.667][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:08.669][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:08.671][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.704][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[2024-05-03 20:28:08.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:08.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:08.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:08.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:08.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:08.907][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 20:28:08.909][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 20:28:08.911][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 20:28:08.925][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 20:28:08.928][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:28:08.931][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 20:28:08.933][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:08.947][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:08.950][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 20:28:08.952][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 20:28:08.954][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:28:08.970][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 20:28:08.973][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:08.975][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:08.977][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 20:28:08.984][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:28:08.986][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 20:28:08.989][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 20:28:08.991][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:28:09.001][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 20:28:09.004][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 20:28:09.006][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 20:28:09.009][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 20:28:09.023][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 20:28:09.026][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 20:28:09.029][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 20:28:09.031][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 20:28:09.041][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 20:28:09.043][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 20:28:09.045][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 20:28:09.047][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 20:28:09.063][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 20:28:09.067][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 20:28:09.070][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 20:28:09.072][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 20:28:09.084][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 20:28:09.086][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 20:28:09.088][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 20:28:09.091][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 20:28:09.096][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 20:28:09.098][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 20:28:09.101][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 20:28:09.103][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 20:28:09.105][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 20:28:09.114][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 20:28:09.117][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 20:28:09.119][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 20:28:09.121][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 20:28:09.131][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 20:28:09.134][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 20:28:09.136][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 20:28:09.139][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 20:28:09.150][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 20:28:09.152][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 20:28:09.155][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 20:28:09.157][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 20:28:09.170][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 20:28:09.173][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 20:28:09.175][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 20:28:09.177][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 20:28:09.191][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 20:28:09.193][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 20:28:09.195][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 20:28:09.197][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 20:28:09.208][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 20:28:09.211][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 20:28:09.213][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:28:09.216][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:28:09.224][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 20:28:09.226][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 20:28:09.228][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 20:28:09.231][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 20:28:09.242][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 20:28:09.245][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 20:28:09.247][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 20:28:09.250][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 20:28:09.260][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 20:28:09.262][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 20:28:09.265][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 20:28:09.267][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 20:28:09.285][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 20:28:09.288][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 20:28:09.290][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 20:28:09.293][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 20:28:09.302][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:09.304][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:09.306][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.309][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.430][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[2024-05-03 20:28:09.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.451][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[2024-05-03 20:28:09.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.489][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[2024-05-03 20:28:09.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:09.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:09.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:09.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:09.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:09.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:09.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:09.505][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:09.506][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:28:09.518][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:09.520][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 20:28:09.522][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:09.523][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:09.524][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:09.525][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:09.526][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:09.527][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:09.528][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:09.529][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:09.530][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:09.532][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-03 20:28:09.533][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-03 20:28:09.534][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-03 20:28:09.535][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:09.536][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:09.536][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:09.537][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:09.537][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:09.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:09.539][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:09.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:09.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:09.541][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:09.542][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-03 20:28:09.542][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-03 20:28:09.543][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:09.544][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:09.546][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:09.546][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:09.547][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-03 20:28:09.549][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:28:09.552][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:28:09.553][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-03 20:28:09.554][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-03 20:28:09.556][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-03 20:28:09.557][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-03 20:28:09.558][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-03 20:28:09.559][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-03 20:28:09.560][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-03 20:28:09.562][biodb::testThat]
biodb.INFO [2024-05-03 20:28:09.563][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-05-03 20:28:09.565][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:09.566][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:09.572][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-03 20:28:09.590][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:09.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-03 20:28:09.594][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:09.688][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-05-03 20:28:11.692][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-05-03 20:28:11.693][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-03 20:28:11.695][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-05-03 20:28:11.696][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-03 20:28:11.698][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-05-03 20:28:11.699][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:28:11.701][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-03 20:28:11.702][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-03 20:28:11.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:11.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:11.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:11.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:11.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:11.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:11.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:11.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:11.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:11.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:11.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:11.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:11.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:11.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:11.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:11.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.730][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:28:11.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:28:11.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.733][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:11.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:11.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:11.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:11.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.741][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:11.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:11.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.744][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:11.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:11.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.747][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:11.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:11.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.752][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:28:11.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:11.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.755][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:28:11.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:11.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.758][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:11.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:11.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.762][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:11.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:11.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.772][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:28:11.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.776][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-03 20:28:11.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.779][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.787][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:28:11.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.805][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:11.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:11.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.822][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:11.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:11.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.826][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:11.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:11.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:11.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:11.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.833][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:11.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:11.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:11.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:11.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:11.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:11.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:11.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:11.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:11.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:11.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:11.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:11.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:11.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:11.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:11.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:11.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:11.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:11.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:11.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:11.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:11.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:11.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:11.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:11.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.886][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:28:11.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-03 20:28:11.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.901][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:11.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:11.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.916][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:11.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:11.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.920][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:11.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:11.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.956][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:11.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:11.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:11.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:11.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.962][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:28:11.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:11.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:11.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:11.977][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-03 20:28:11.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.015][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.041][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.098][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:28:12.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.102][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-03 20:28:12.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.188][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-03 20:28:12.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.191][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.194][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.201][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:12.247][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-05-03 20:28:12.249][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:28:12.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:12.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:12.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:12.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:12.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:12.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:12.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:12.261][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:28:12.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:28:12.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.265][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:28:12.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:28:12.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.268][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 20:28:12.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 20:28:12.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.272][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 20:28:12.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 20:28:12.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.275][private$selectFields] Fields none
biodb.TRACE[2024-05-03 20:28:12.276][private$selectFields]
biodb.TRACE[2024-05-03 20:28:12.277][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-03 20:28:12.278][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:28:12.279][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:12.279][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.280][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.282][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.282][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.283][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.285][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.285][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.286][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.301][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.301][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.302][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.304][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.304][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.305][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.307][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.307][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.308][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.310][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.311][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.313][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.314][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.315][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.317][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.319][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.321][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.322][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.324][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.324][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.325][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.327][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.327][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.328][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.330][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.330][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.332][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.334][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.335][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.336][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.337][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.338][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.340][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.341][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.341][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.343][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.345][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:12.346][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:12.347][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.347][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.349][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.350][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.351][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.352][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.353][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.354][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.357][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.357][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.358][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.360][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.361][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.362][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.363][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.364][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.365][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.368][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.369][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.371][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.373][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.375][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.376][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.382][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.384][private$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[2024-05-03 20:28:12.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.430][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.436][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.451][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.487][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.505][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.508][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.511][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.553][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-05-03 20:28:12.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:12.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:12.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:12.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:12.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:12.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:12.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:12.564][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:28:12.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:28:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:28:12.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:28:12.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.571][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 20:28:12.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 20:28:12.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.574][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 20:28:12.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 20:28:12.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.577][private$selectFields] Fields none
biodb.TRACE[2024-05-03 20:28:12.578][private$selectFields]
biodb.TRACE[2024-05-03 20:28:12.578][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-03 20:28:12.579][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:28:12.580][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:12.581][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.584][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.584][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.585][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.587][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.587][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.588][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.590][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.591][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.593][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.594][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.595][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.596][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.597][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.598][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.599][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.600][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.602][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.604][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.605][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.607][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.608][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.610][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.610][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.611][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.612][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.613][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.614][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.615][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.616][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.617][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.619][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.620][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.621][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.622][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.623][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.624][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.625][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.626][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.627][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.629][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.630][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.630][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.632][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.633][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:12.634][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-03 20:28:12.634][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.635][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.637][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.638][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.651][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.652][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.653][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.655][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.655][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.656][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.658][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.659][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.659][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.661][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.662][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.663][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.665][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.666][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.666][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.668][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.669][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.670][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.671][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.672][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-05-03 20:28:12.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:12.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:12.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:12.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.695][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.710][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.713][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-03 20:28:12.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.716][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.723][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-03 20:28:12.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:12.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.741][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:12.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:12.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:12.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:12.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.794][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.797][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-03 20:28:12.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:12.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:12.804][private$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[2024-05-03 20:28:12.805][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:28:12.806][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-05-03 20:28:12.811][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 20:28:12.812][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-03 20:28:12.813][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-03 20:28:12.814][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 20:28:12.815][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:12.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:12.817][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:12.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:12.818][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:12.819][FUN] Functions in observer 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 161 ]

══ 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 161 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn 2.597 1.39112.949
LipidmapsStructureEntry0.3390.0291.052