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This page was generated on 2024-05-18 11:37:36 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for biodbLipidmaps on 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: 2024-05-17 19:24:16 -0400 (Fri, 17 May 2024)
EndedAt: 2024-05-17 19:28:41 -0400 (Fri, 17 May 2024)
EllapsedTime: 265.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/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 (2024-04-24) -- "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 [2024-05-17 19:25:15.096][biodb::testContext]
biodb.INFO [2024-05-17 19:25:15.101][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 19:25:15.103][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-17 19:25:15.104][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 19:25:15.106][biodb::testContext]
biodb.INFO [2024-05-17 19:25:15.115][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-17 19:25:15.118][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-17 19:25:15.128][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:25:15.130][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-17 19:25:15.131][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-17 19:25:15.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.135][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-17 19:25:15.161][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-17 19:25:15.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.167][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-17 19:25:15.169][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-17 19:25:15.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.175][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-17 19:25:15.177][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-17 19:25:15.178][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-17 19:25:15.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.197][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-17 19:25:15.198][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-17 19:25:15.200][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-17 19:25:15.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.204][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-17 19:25:15.205][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-17 19:25:15.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.210][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-17 19:25:15.211][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-17 19:25:15.212][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-17 19:25:15.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.217][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-17 19:25:15.219][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-17 19:25:15.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.223][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-17 19:25:15.224][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-17 19:25:15.225][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-17 19:25:15.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.229][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-17 19:25:15.230][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-17 19:25:15.231][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-17 19:25:15.233][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-17 19:25:15.234][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-17 19:25:15.235][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-17 19:25:15.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.240][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-17 19:25:15.241][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-17 19:25:15.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.246][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-17 19:25:15.247][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-17 19:25:15.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.251][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-17 19:25:15.252][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-17 19:25:15.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.256][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-17 19:25:15.257][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-17 19:25:15.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.259][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.DEBUG[2024-05-17 19:25:15.261][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-17 19:25:15.262][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-17 19:25:15.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.266][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-17 19:25:15.267][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-17 19:25:15.291][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-17 19:25:15.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.296][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-17 19:25:15.298][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-17 19:25:15.299][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-17 19:25:15.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.306][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-17 19:25:15.351][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.373][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-17 19:25:15.374][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.376][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:25:15.377][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.378][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.380][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.381][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.383][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:25:15.384][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:25:15.385][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.387][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-17 19:25:15.388][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:25:15.390][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.391][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.392][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:25:15.392][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:25:15.392][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 19:25:15.392][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 19:25:15.392][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 19:25:15.393][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:25:15.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.397][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:25:15.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.399][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.400][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.401][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.403][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:25:15.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:25:15.405][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.406][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.407][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-17 19:25:15.409][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.409][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 19:25:15.410][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.412][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:25:15.413][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.414][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.416][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.417][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.418][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 19:25:15.419][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:25:15.421][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.422][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-17 19:25:15.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:25:15.425][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.426][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:25:15.426][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:25:15.426][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 19:25:15.426][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 19:25:15.426][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 19:25:15.427][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:25:15.428][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.429][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.431][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:25:15.432][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.434][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.435][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.436][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.437][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:25:15.438][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:25:15.439][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.440][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.442][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-17 19:25:15.444][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.445][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-17 19:25:15.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.447][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:25:15.448][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.449][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.450][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.451][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.452][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:25:15.453][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:25:15.454][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.456][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-17 19:25:15.462][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:25:15.463][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.464][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.465][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.466][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:25:15.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.469][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:25:15.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.474][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:25:15.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:25:15.477][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.479][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.480][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-17 19:25:15.482][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.483][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 19:25:15.484][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.485][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:25:15.487][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.488][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.489][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.491][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.492][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 19:25:15.493][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:25:15.495][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.496][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-17 19:25:15.497][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:25:15.498][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.500][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.501][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.502][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:25:15.504][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.505][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.506][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:25:15.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.511][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.512][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:25:15.513][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:25:15.513][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.514][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.519][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:25:15.520][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.535][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.DEBUG[2024-05-17 19:25:15.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.613][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-17 19:25:15.619][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-17 19:25:15.621][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-17 19:25:15.622][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-17 19:25:15.624][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 19:25:15.625][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-17 19:25:15.627][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-17 19:25:15.629][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-17 19:25:15.631][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-17 19:25:15.632][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-17 19:25:15.633][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 19:25:15.635][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-17 19:25:15.636][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-17 19:25:15.638][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-17 19:25:15.640][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-17 19:25:15.641][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 19:25:15.642][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-17 19:25:15.644][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-17 19:25:15.646][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 19:25:15.647][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-17 19:25:15.649][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-17 19:25:15.651][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-17 19:25:15.653][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-17 19:25:15.655][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-17 19:25:15.657][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-17 19:25:15.658][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-17 19:25:15.660][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-17 19:25:15.662][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-17 19:25:15.663][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-17 19:25:15.665][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-17 19:25:15.667][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-17 19:25:15.669][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-17 19:25:15.673][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-17 19:25:15.675][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-17 19:25:15.677][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-17 19:25:15.679][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-17 19:25:15.681][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-17 19:25:15.683][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-17 19:25:15.685][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-17 19:25:15.686][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-17 19:25:15.687][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-17 19:25:15.689][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-17 19:25:15.690][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-17 19:25:15.691][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-17 19:25:15.693][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-17 19:25:15.694][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-17 19:25:15.696][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-17 19:25:15.703][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-17 19:25:15.705][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-17 19:25:15.707][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-17 19:25:15.708][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-17 19:25:15.711][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-17 19:25:15.712][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-17 19:25:15.713][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-17 19:25:15.715][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-17 19:25:15.717][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-17 19:25:15.719][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-17 19:25:15.721][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-17 19:25:15.722][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-17 19:25:15.724][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-17 19:25:15.726][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-17 19:25:15.728][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-17 19:25:15.729][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-17 19:25:15.730][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-17 19:25:15.732][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-17 19:25:15.734][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-17 19:25:15.735][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 19:25:15.737][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 19:25:15.738][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-17 19:25:15.740][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-17 19:25:15.741][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-17 19:25:15.743][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-17 19:25:15.745][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-17 19:25:15.747][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-17 19:25:15.748][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-17 19:25:15.751][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-17 19:25:15.752][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-17 19:25:15.754][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-17 19:25:15.755][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-17 19:25:15.757][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-17 19:25:15.759][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-17 19:25:15.761][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-17 19:25:15.763][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-17 19:25:15.771][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-17 19:25:15.773][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-17 19:25:15.777][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:25:15.778][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.781][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.805][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.DEBUG[2024-05-17 19:25:15.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.832][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[2024-05-17 19:25:15.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.841][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[2024-05-17 19:25:15.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.878][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[2024-05-17 19:25:15.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.892][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[2024-05-17 19:25:15.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:25:15.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:15.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:15.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:15.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:15.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:15.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:15.911][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-17 19:25:15.922][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:25:15.930][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.931][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.932][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.933][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:25:15.934][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.936][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.937][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.939][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:25:15.940][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:25:15.941][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.942][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-17 19:25:15.944][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-17 19:25:15.945][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-17 19:25:15.947][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-17 19:25:15.948][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:25:15.948][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:25:15.949][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:25:15.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.951][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.952][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:25:15.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:25:15.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:25:15.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:25:15.956][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-17 19:25:15.956][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-17 19:25:15.957][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:25:15.958][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:25:15.959][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-17 19:25:15.961][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:25:15.969][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-17 19:25:15.971][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 19:25:16.006][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:25:16.008][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-17 19:25:16.014][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:25:16.018][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-17 19:25:16.023][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-17 19:25:16.025][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-17 19:25:16.027][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-17 19:25:16.028][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-17 19:25:16.041][biodb::testThat]
biodb.INFO [2024-05-17 19:25:16.042][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-17 19:25:16.043][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:16.044][biodb::testThat]
biodb.TRACE[2024-05-17 19:25:16.049][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[2024-05-17 19:25:16.051][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-17 19:25:16.054][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-17 19:25:16.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:25:16.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:16.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:16.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:16.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:16.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:16.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:25:16.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:25:16.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:25:16.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.128][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:25:16.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:25:16.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.134][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:25:16.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:25:16.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.138][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.171][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.196][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:25:16.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.201][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:25:16.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.205][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:16.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:16.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:16.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:16.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.225][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:25:16.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.229][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-17 19:25:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.241][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:25:16.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.316][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.320][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.329][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:25:16.395][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-17 19:25:16.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:25:16.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:25:16.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.402][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:25:16.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:25:16.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.407][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-17 19:25:16.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-17 19:25:16.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.412][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-17 19:25:16.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-17 19:25:16.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.501][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.510][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:16.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.537][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.538][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.539][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.566][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.567][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.570][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.591][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.595][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.599][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.603][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.604][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.606][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.607][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.619][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:16.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:16.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.623][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:16.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:16.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.628][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:16.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:16.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.634][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:16.635][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:16.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.637][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:16.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:16.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.668][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.670][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.691][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.696][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.702][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.703][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.705][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.718][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:16.719][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:16.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.721][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.728][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.729][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:16.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.732][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.740][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:16.741][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:16.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.744][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.751][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.752][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:16.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.755][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.762][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:16.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:16.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.766][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:16.772][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.773][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:16.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:16.775][ef$get] fields variable is a list.
biodb.INFO [2024-05-17 19:25:16.788][biodb::testThat]
biodb.INFO [2024-05-17 19:25:16.789][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-17 19:25:16.790][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:16.797][biodb::testThat]
biodb.DEBUG[2024-05-17 19:25:16.815][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-05-17 19:25:16.825][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 19:25:16.830][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.INFO [2024-05-17 19:25:16.832][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-05-17 19:25:16.833][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 19:25:16.835][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 19:25:16.836][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 19:25:16.837][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-17 19:25:16.838][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 19:25:16.839][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 19:25:16.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:25:16.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:16.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:16.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:16.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:16.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:16.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:16.858][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-05-17 19:25:16.881][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:25:16.882][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:25:16.883][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-17 19:25:18.176][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2024-05-17 19:25:19.072][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-05-17 19:25:19.075][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-05-17 19:25:19.077][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2024-05-17 19:25:19.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2024-05-17 19:25:19.100][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2024-05-17 19:25:19.102][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 19:25:19.127][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-17 19:25:19.128][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-17 19:25:19.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:25:19.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:19.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:19.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:19.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:19.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:19.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:25:19.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:25:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:25:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:25:19.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:25:19.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.169][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:25:19.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:25:19.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.172][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:25:19.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:25:19.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.176][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:19.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:19.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.193][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:19.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:25:19.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.198][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:19.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:19.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.203][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:19.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:25:19.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.207][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:25:19.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:19.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.212][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:25:19.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:19.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.216][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:19.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:19.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:25:19.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:25:19.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.234][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:25:19.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.238][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-17 19:25:19.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.250][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:25:19.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:19.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:19.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:19.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:19.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.294][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:19.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:25:19.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:25:19.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:25:19.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:25:19.323][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-17 19:25:19.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-17 19:25:19.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-17 19:25:19.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-17 19:25:19.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-17 19:25:19.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-17 19:25:19.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-17 19:25:19.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 19:25:19.356][biodb::testThat]
biodb.INFO [2024-05-17 19:25:19.357][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-17 19:25:19.359][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:19.360][biodb::testThat]
biodb.TRACE[2024-05-17 19:25:19.364][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.365][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.368][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:25:19.370][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-05-17 19:25:19.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:19.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:19.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:19.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:19.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:25:19.417][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-17 19:25:19.448][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[2024-05-17 19:25:19.468][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:25:19.469][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:25:19.493][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-05-17 19:25:20.121][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-05-17 19:25:20.707][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:25:20.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-05-17 19:25:20.716][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-05-17 19:25:20.719][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-05-17 19:25:20.741][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:20.742][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:20.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:20.744][ef$get] fields variable is a list.
biodb.INFO [2024-05-17 19:25:20.751][biodb::testThat]
biodb.INFO [2024-05-17 19:25:20.752][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-17 19:25:20.754][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:20.755][biodb::testThat]
biodb.TRACE[2024-05-17 19:25:20.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:20.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:20.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:20.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:20.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:20.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:20.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:20.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:20.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:20.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:20.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:20.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:25:20.931][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-17 19:25:20.936][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 19:25:20.961][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-17 19:25:20.963][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 19:25:20.966][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-05-17 19:25:21.000][biodb::testThat]
biodb.INFO [2024-05-17 19:25:21.002][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-17 19:25:21.004][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:21.005][biodb::testThat]
biodb.TRACE[2024-05-17 19:25:21.043][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:25:21.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:25:21.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:21.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:21.050][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:25:21.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:25:21.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:21.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:21.055][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-17 19:25:21.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-17 19:25:21.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:21.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:21.060][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-17 19:25:21.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-17 19:25:21.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:21.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:21.128][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:25:21.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:25:21.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:21.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:21.133][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:25:21.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:25:21.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:21.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:21.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-17 19:25:21.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-17 19:25:21.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:21.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:21.145][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-17 19:25:21.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-17 19:25:21.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:21.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 19:25:21.159][biodb::testThat]
biodb.INFO [2024-05-17 19:25:21.161][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-17 19:25:21.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:21.164][biodb::testThat]
biodb.INFO [2024-05-17 19:25:21.177][biodb::testThat]
biodb.INFO [2024-05-17 19:25:21.179][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-17 19:25:21.180][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:21.181][biodb::testThat]
biodb.INFO [2024-05-17 19:25:21.193][biodb::testThat]
biodb.INFO [2024-05-17 19:25:21.195][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-17 19:25:21.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:21.199][biodb::testThat]
biodb.DEBUG[2024-05-17 19:25:21.205][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-05-17 19:25:21.979][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-05-17 19:25:22.415][biodb::testThat]
biodb.INFO [2024-05-17 19:25:22.417][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-17 19:25:22.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:22.420][biodb::testThat]
biodb.TRACE[2024-05-17 19:25:22.430][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:22.432][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:22.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:22.435][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:22.436][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:22.438][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:22.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:22.441][ef$get] fields variable is a list.
biodb.INFO [2024-05-17 19:25:22.443][biodb::testThat]
biodb.INFO [2024-05-17 19:25:22.444][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-17 19:25:22.445][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:22.447][biodb::testThat]
biodb.TRACE[2024-05-17 19:25:22.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:22.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:22.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:22.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:22.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:22.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:22.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:22.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:22.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:25:22.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:25:22.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:22.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:25:22.748][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-17 19:25:22.753][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 19:25:22.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-17 19:25:22.763][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 19:25:22.766][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-17 19:25:22.938][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-17 19:25:22.950][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 19:25:22.952][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-17 19:25:22.954][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 19:25:22.956][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-05-17 19:25:22.985][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-17 19:25:22.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-17 19:25:22.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:22.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:23.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 19:25:23.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 19:25:23.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:23.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:23.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:23.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:23.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:23.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:23.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:23.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:23.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:23.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:23.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:23.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:23.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:25:23.130][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-17 19:25:23.139][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:25:23.141][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:25:23.144][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-17 19:25:27.240][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-05-17 19:25:40.400][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:25:40.415][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-05-17 19:25:40.498][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-05-17 19:25:42.203][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[2024-05-17 19:25:42.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:25:42.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:25:42.210][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-17 19:25:42.783][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-05-17 19:25:43.413][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:25:43.416][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-05-17 19:25:43.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-05-17 19:25:43.456][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-05-17 19:25:43.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:25:43.462][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:25:43.465][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-05-17 19:25:44.095][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-05-17 19:25:44.715][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:25:44.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-05-17 19:25:44.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-05-17 19:25:44.751][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-17 19:25:44.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-17 19:25:44.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:44.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 19:25:44.770][biodb::testThat]
biodb.INFO [2024-05-17 19:25:44.771][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-17 19:25:44.773][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:25:44.774][biodb::testThat]
biodb.TRACE[2024-05-17 19:25:44.778][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-17 19:25:44.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-17 19:25:44.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:44.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:44.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 19:25:44.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 19:25:44.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:44.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:44.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:44.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:44.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:44.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:44.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:44.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:44.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:44.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:44.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:44.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:44.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:44.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:25:44.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:44.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:25:44.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:25:44.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:25:44.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:25:44.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:25:44.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:25:44.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:25:44.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:25:44.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:25:44.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:25:44.836][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[2024-05-17 19:25:44.840][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:25:44.842][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:25:44.845][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-05-17 19:25:48.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-05-17 19:26:01.856][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:26:01.904][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-05-17 19:26:02.170][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-05-17 19:26:05.467][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-05-17 19:26:05.500][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-17 19:26:05.503][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-05-17 19:26:05.504][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-17 19:26:05.505][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 19:26:05.506][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 19:26:05.507][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-17 19:26:05.508][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 19:26:05.508][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 19:26:05.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:05.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:05.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:05.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:05.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:05.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:05.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:26:05.561][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-05-17 19:26:05.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:05.564][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:05.565][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-17 19:26:06.200][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-05-17 19:26:06.833][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:26:06.846][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-05-17 19:26:06.880][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-05-17 19:26:06.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:06.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:06.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:06.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:06.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:06.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:06.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:26:06.902][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-05-17 19:26:06.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:06.905][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:06.907][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-05-17 19:26:07.544][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-05-17 19:26:08.289][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:26:08.293][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-05-17 19:26:08.356][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-05-17 19:26:08.362][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-05-17 19:26:08.364][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 19:26:08.366][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-17 19:26:08.367][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-17 19:26:08.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:08.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:08.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:08.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:08.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:08.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:08.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:26:08.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:08.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:08.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:08.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:08.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:08.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:08.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:08.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:08.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:26:08.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:26:08.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:08.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:08.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:26:08.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:26:08.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:08.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:08.878][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:26:08.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:26:08.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:08.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:08.924][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:26:08.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:26:08.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:08.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:08.928][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:26:08.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:26:08.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:08.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.018][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:26:09.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:26:09.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:26:09.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:26:09.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:26:09.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:26:09.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.335][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:26:09.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:09.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.421][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:26:09.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:09.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.505][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:26:09.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:26:09.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.612][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:26:09.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:26:09.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:26:09.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:09.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:26:09.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:09.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.829][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:26:09.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:09.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.891][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-17 19:26:09.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:09.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:26:09.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:09.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:26:09.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:09.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:09.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:09.961][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:26:09.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:10.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.010][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.016][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.098][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:26:10.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:10.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:10.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:10.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:10.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:10.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:10.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:26:10.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:26:10.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:26:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.293][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:26:10.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:26:10.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.300][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:26:10.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:26:10.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.311][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:26:10.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:26:10.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.318][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:26:10.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:26:10.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:26:10.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:26:10.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:26:10.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:26:10.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.342][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:26:10.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.351][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:26:10.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.359][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:26:10.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:26:10.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:26:10.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:26:10.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:26:10.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:10.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:26:10.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:10.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.392][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:26:10.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:10.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.398][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-17 19:26:10.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:10.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:26:10.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:10.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:26:10.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:10.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.416][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:26:10.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:26:10.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.421][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.439][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.446][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:26:10.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:26:10.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:26:10.489][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-05-17 19:26:10.497][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 19:26:10.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:10.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:10.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:10.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:10.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:10.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:10.523][FUN] Functions in observer BiodbConfig: [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[2024-05-17 19:26:10.524][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.528][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.532][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.533][private$selectFields]
biodb.TRACE[2024-05-17 19:26:10.545][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:10.546][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:10.547][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.547][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.548][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.550][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.551][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.553][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.555][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.555][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.556][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.557][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.558][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.560][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.560][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:10.561][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.565][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.569][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.583][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-17 19:26:10.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:10.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:10.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:10.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:10.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:10.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:10.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:26:10.595][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.599][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.604][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.608][private$selectFields]
biodb.TRACE[2024-05-17 19:26:10.609][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:10.610][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:10.610][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.611][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.613][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.615][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.616][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.618][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.620][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.621][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.622][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.624][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.625][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.627][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.627][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:10.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.633][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.638][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.642][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-17 19:26:10.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:10.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:10.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:10.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:10.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:10.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:10.666][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.TRACE[2024-05-17 19:26:10.669][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.675][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.680][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.682][private$selectFields]
biodb.TRACE[2024-05-17 19:26:10.683][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:10.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:10.686][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.687][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.688][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.689][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.690][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.691][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.693][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.694][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.695][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:10.695][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.697][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.699][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.700][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:10.701][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.704][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.707][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:10.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.723][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-17 19:26:10.728][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 19:26:10.729][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 19:26:10.744][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-17 19:26:10.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-17 19:26:10.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 19:26:10.756][biodb::testThat]
biodb.INFO [2024-05-17 19:26:10.757][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-17 19:26:10.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:26:10.760][biodb::testThat]
biodb.TRACE[2024-05-17 19:26:10.764][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-17 19:26:10.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-17 19:26:10.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 19:26:10.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 19:26:10.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:10.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:10.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:10.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:26:10.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:10.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:10.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:10.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:10.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:10.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:10.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:26:10.852][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[2024-05-17 19:26:10.855][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:10.856][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:10.857][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-05-17 19:26:14.745][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-05-17 19:26:33.659][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:26:33.692][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-05-17 19:26:33.847][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-05-17 19:26:43.310][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 19:26:43.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:43.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:43.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:43.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:43.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:43.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:43.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:26:43.409][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.415][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.481][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.483][private$selectFields]
biodb.TRACE[2024-05-17 19:26:43.485][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:43.487][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:43.489][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.491][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.493][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.496][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.498][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.499][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.502][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.504][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.524][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.526][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.530][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.533][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.543][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:43.548][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.561][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.565][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.578][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-17 19:26:43.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:43.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:43.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:43.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:43.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:43.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:43.612][FUN] Functions in observer BiodbConfig: [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[2024-05-17 19:26:43.647][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.678][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.680][private$selectFields]
biodb.TRACE[2024-05-17 19:26:43.683][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:43.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:43.688][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.689][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.696][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.699][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.723][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.725][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.728][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.729][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.732][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.735][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.737][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.740][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.741][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:43.743][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.759][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.833][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.855][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-17 19:26:43.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:43.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:43.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:43.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:43.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:43.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:43.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:26:43.899][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.904][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.922][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.923][private$selectFields]
biodb.TRACE[2024-05-17 19:26:43.926][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:43.928][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:43.929][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.931][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.956][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.960][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.972][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.974][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:43.976][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:43.977][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.979][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:43.981][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:43.986][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:44.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.031][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.033][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:44.034][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:44.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:44.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:44.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:44.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.101][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:44.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:44.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.121][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-17 19:26:44.123][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 19:26:44.125][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 19:26:44.314][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-17 19:26:44.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-17 19:26:44.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 19:26:44.388][biodb::testThat]
biodb.INFO [2024-05-17 19:26:44.403][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-17 19:26:44.404][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:26:44.418][biodb::testThat]
biodb.TRACE[2024-05-17 19:26:44.442][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-17 19:26:44.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-17 19:26:44.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-17 19:26:44.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-17 19:26:44.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:44.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:44.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:44.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:44.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:44.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:44.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:44.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:44.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:26:44.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:44.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:26:44.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:44.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:44.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:44.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:44.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:44.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:44.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:26:44.545][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-17 19:26:44.551][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 19:26:44.578][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-17 19:26:44.580][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 19:26:44.872][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-17 19:26:49.262][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 19:26:49.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:49.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:49.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:49.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:49.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:49.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:49.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:26:49.296][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.300][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.303][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.304][private$selectFields]
biodb.TRACE[2024-05-17 19:26:49.305][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:49.306][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:49.307][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.308][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.309][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.310][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.311][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.312][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.313][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.314][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.316][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.317][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.318][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.319][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.320][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:49.321][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.325][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.329][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.333][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-17 19:26:49.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:49.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:49.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:49.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:49.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:49.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:49.344][FUN] Functions in observer BiodbConfig: [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[2024-05-17 19:26:49.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.349][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.354][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.355][private$selectFields]
biodb.TRACE[2024-05-17 19:26:49.356][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:49.356][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:49.357][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.358][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.359][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.362][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.362][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.363][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.365][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.366][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.367][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.367][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.369][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.370][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.371][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:49.372][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.376][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.379][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.383][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-17 19:26:49.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:49.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:49.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:49.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:49.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:49.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:49.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:26:49.431][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.435][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.439][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.440][private$selectFields]
biodb.TRACE[2024-05-17 19:26:49.441][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-17 19:26:49.442][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:26:49.443][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.444][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.445][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.448][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.450][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.451][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.453][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.454][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.455][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:26:49.458][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.469][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.471][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.472][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-17 19:26:49.495][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.500][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.504][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:26:49.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:26:49.507][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-17 19:26:49.508][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 19:26:49.509][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-17 19:26:49.623][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-17 19:26:49.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-17 19:26:49.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:26:49.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-17 19:26:49.666][biodb::testThat]
biodb.INFO [2024-05-17 19:26:49.667][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-17 19:26:49.668][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:26:49.669][biodb::testThat]
biodb.DEBUG[2024-05-17 19:26:49.677][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-17 19:26:49.678][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-17 19:26:49.679][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-17 19:26:49.681][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-17 19:26:49.682][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 19:26:49.682][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 19:26:49.684][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-17 19:26:49.685][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 19:26:49.686][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 19:26:49.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:26:49.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:26:49.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:26:49.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:26:49.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:26:49.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:26:49.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:26:49.737][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-05-17 19:26:49.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:49.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:49.742][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:26:50.397][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:26:50.400][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:26:50.402][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:26:50.404][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:26:51.075][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:26:51.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:51.078][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:51.079][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:26:51.696][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:26:51.697][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:26:51.699][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:26:51.701][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:26:52.332][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:26:52.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:52.334][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:52.391][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:26:52.996][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:26:52.997][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:26:52.998][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:26:52.999][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:26:53.586][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:26:53.588][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:53.589][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:53.591][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:26:54.219][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:26:54.231][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:26:54.244][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:26:54.245][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:26:54.891][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:26:54.892][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:54.893][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:54.894][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:26:55.496][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:26:55.497][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:26:55.530][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:26:55.531][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:26:56.150][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:26:56.152][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:56.154][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:56.156][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:26:56.749][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:26:56.763][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:26:56.764][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:26:56.765][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:26:57.393][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:26:57.395][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:57.396][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:57.408][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:26:58.033][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:26:58.034][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:26:58.035][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:26:58.036][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:26:58.887][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:26:58.889][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:26:58.891][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:26:58.893][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:26:59.526][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:26:59.528][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:26:59.530][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:26:59.531][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:27:00.096][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:00.097][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:00.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:00.100][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:27:00.674][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:00.692][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:00.694][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:00.695][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:27:01.268][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:01.270][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:01.272][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:01.274][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-17 19:27:01.918][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:01.933][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:01.934][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:01.935][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-17 19:27:02.528][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-17 19:27:02.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-05-17 19:27:02.559][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 19:27:02.583][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-17 19:27:02.584][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-17 19:27:02.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:27:02.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:27:02.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:27:02.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:27:02.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:27:02.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:27:02.597][FUN] Functions in observer BiodbConfig: [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[2024-05-17 19:27:02.599][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:02.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:02.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:02.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:02.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:02.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:02.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:02.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:02.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:02.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:02.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:02.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:02.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:02.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:02.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:02.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:02.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:02.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:02.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:02.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:02.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:02.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:02.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:02.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:02.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:02.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:02.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:02.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:02.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:02.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:02.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:02.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:27:02.638][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-17 19:27:02.639][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-17 19:27:02.650][biodb::testThat]
biodb.INFO [2024-05-17 19:27:02.651][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-17 19:27:02.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:27:02.653][biodb::testThat]
biodb.DEBUG[2024-05-17 19:27:02.710][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-05-17 19:27:02.711][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-05-17 19:27:02.712][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-17 19:27:02.714][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-05-17 19:27:02.715][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-17 19:27:02.716][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-17 19:27:02.717][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 19:27:02.718][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-17 19:27:02.719][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-17 19:27:02.720][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-17 19:27:02.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:27:02.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:27:02.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:27:02.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:27:02.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:27:02.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:27:02.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:27:02.736][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-05-17 19:27:02.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:02.739][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:02.741][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:03.306][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:03.307][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:03.309][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:03.311][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:03.967][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:03.969][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:03.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:03.972][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:04.537][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:04.538][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:04.539][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:04.540][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:05.118][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:05.120][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:05.121][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:05.123][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:05.696][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:05.699][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:05.700][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:05.702][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:06.588][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:06.590][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:06.591][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:06.593][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:07.141][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:07.154][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:07.156][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:07.158][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:07.829][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:07.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:07.841][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:07.843][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:08.402][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:08.404][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:08.405][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:08.406][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:08.973][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:08.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:08.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:08.976][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:09.548][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:09.549][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:09.550][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:09.551][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:10.095][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:10.096][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:10.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:10.097][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:10.659][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:10.660][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:10.662][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:10.663][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:11.234][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:11.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:11.237][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:11.240][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:11.803][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:11.805][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:11.806][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:11.808][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:12.480][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:12.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:12.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:12.491][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:13.089][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:13.103][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:13.105][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:13.107][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:13.973][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:13.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:13.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:13.976][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-17 19:27:14.539][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:14.540][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:14.541][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:14.544][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-17 19:27:15.369][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:15.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:27:15.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:27:15.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:27:15.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:27:15.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:27:15.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:27:15.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:27:15.394][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-05-17 19:27:15.399][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:15.400][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:15.402][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:15.965][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:15.966][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:15.968][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:15.969][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:16.521][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:16.523][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:16.531][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:16.546][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:17.149][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:17.151][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:17.152][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:17.155][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:18.158][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:18.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:18.446][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:18.465][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:19.066][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:19.083][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:19.115][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:19.149][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:20.426][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:20.439][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:20.441][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:20.468][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:21.049][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:21.051][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:21.056][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:21.058][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:21.639][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:21.640][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:21.643][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:21.646][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:22.248][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:22.270][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:22.292][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:22.297][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:22.853][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:22.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:22.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:22.871][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:23.742][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:23.744][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:23.745][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:23.748][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:24.625][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:24.626][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:24.627][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:24.629][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:25.207][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:25.208][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:25.223][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:25.249][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:25.819][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:25.826][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:25.833][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:25.836][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:26.406][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:26.409][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:26.423][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:26.465][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:27.180][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:27.199][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:27.202][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:27.224][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:27.944][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:28.046][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:28.061][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:28.173][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:28.913][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-17 19:27:28.995][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:29.052][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:29.065][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-17 19:27:29.957][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-17 19:27:30.057][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-17 19:27:30.106][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-17 19:27:30.155][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-17 19:27:30.869][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-17 19:27:30.988][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-05-17 19:27:31.029][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-17 19:27:31.065][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-17 19:27:31.084][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-17 19:27:31.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:27:31.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:27:31.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:27:31.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:27:31.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:27:31.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:27:31.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:27:31.366][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:31.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:33.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.105][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:33.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:33.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:33.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:33.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:27:33.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:27:33.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:27:33.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:27:33.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:27:33.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:27:33.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:27:33.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:27:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:33.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:33.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.706][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:33.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:27:33.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:33.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:33.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:33.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:33.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:33.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:33.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:33.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:33.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:33.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:33.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:33.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:33.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:33.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:34.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:34.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:34.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:34.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:34.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:34.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:34.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:34.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:34.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:34.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:34.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:34.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:34.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:34.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:34.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:34.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:27:35.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:27:35.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:27:35.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:27:35.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:27:35.340][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-17 19:27:35.462][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-17 19:27:35.540][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-05-17 19:27:40.145][biodb::testThat]
biodb.INFO [2024-05-17 19:27:40.150][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-17 19:27:40.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:27:40.165][biodb::testThat]
biodb.INFO [2024-05-17 19:27:40.505][biodb::testThat]
biodb.INFO [2024-05-17 19:27:40.507][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-17 19:27:40.533][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:27:40.547][biodb::testThat]
biodb.INFO [2024-05-17 19:27:40.637][biodb::testThat]
biodb.INFO [2024-05-17 19:27:40.639][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-17 19:27:40.650][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:27:40.653][biodb::testThat]
biodb.DEBUG[2024-05-17 19:27:40.660][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[2024-05-17 19:27:40.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:27:40.664][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:27:40.668][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-05-17 19:27:44.773][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-05-17 19:27:58.252][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:27:58.255][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-05-17 19:27:58.520][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-05-17 19:28:01.411][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:01.412][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:01.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:01.413][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:01.414][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:01.415][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:01.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:01.417][ef$get] fields variable is a list.
biodb.INFO [2024-05-17 19:28:01.425][biodb::testThat]
biodb.INFO [2024-05-17 19:28:01.426][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-17 19:28:01.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:28:01.428][biodb::testThat]
biodb.ERROR[2024-05-17 19:28:01.449][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-17 19:28:01.482][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-17 19:28:01.506][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-17 19:28:01.507][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-17 19:28:01.508][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-17 19:28:01.509][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-17 19:28:01.509][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:01.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:01.511][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:01.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:01.513][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-17 19:28:01.533][biodb::testContext]
biodb.INFO [2024-05-17 19:28:01.534][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 19:28:01.535][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-05-17 19:28:01.550][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 19:28:01.551][biodb::testContext]
biodb.INFO [2024-05-17 19:28:01.556][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-17 19:28:01.557][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-17 19:28:01.571][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:28:01.572][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-17 19:28:01.573][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-17 19:28:01.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.576][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-17 19:28:01.577][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-17 19:28:01.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.580][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-17 19:28:01.581][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-17 19:28:01.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.584][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-17 19:28:01.585][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-17 19:28:01.586][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-17 19:28:01.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.589][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-17 19:28:01.590][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-17 19:28:01.601][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-17 19:28:01.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.605][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-17 19:28:01.608][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-17 19:28:01.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.611][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-17 19:28:01.612][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-17 19:28:01.613][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-17 19:28:01.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.616][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-17 19:28:01.617][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-17 19:28:01.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.620][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-17 19:28:01.621][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-17 19:28:01.622][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-17 19:28:01.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.625][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-17 19:28:01.626][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-17 19:28:01.627][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-17 19:28:01.628][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-17 19:28:01.629][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-17 19:28:01.630][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-17 19:28:01.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.638][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-17 19:28:01.639][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-17 19:28:01.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.642][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-17 19:28:01.642][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-17 19:28:01.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.646][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-17 19:28:01.646][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-17 19:28:01.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.649][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[2024-05-17 19:28:01.649][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-17 19:28:01.651][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-17 19:28:01.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.654][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-17 19:28:01.666][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-17 19:28:01.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.670][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-17 19:28:01.671][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-17 19:28:01.850][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-17 19:28:01.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:01.866][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-17 19:28:01.867][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-17 19:28:01.868][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-17 19:28:01.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:01.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:01.894][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[2024-05-17 19:28:01.896][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-17 19:28:01.898][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:01.898][self$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[2024-05-17 19:28:01.900][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:01.901][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:01.902][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:01.904][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:01.905][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:01.906][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:01.907][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:28:01.908][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:01.909][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:01.911][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-17 19:28:01.913][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:01.914][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:01.916][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:01.923][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:28:01.923][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:28:01.923][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 19:28:01.923][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 19:28:01.923][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 19:28:01.948][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:01.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:01.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:01.983][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:01.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:01.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:01.992][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.000][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:02.009][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:02.010][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.011][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.013][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-17 19:28:02.015][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.016][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 19:28:02.055][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.057][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:02.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.060][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.061][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.062][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.063][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 19:28:02.064][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:02.065][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.066][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-17 19:28:02.067][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:02.069][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.070][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.072][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:28:02.072][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:28:02.072][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 19:28:02.072][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 19:28:02.072][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 19:28:02.072][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:02.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:02.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:02.077][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:02.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:02.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:02.083][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.084][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.085][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:02.086][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:02.087][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.088][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.089][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-17 19:28:02.091][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.122][self$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[2024-05-17 19:28:02.123][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.124][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:02.125][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.127][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.128][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.129][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:28:02.130][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:02.136][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.137][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-17 19:28:02.139][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:02.140][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.141][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.142][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.143][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:02.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:02.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:02.178][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:02.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:02.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:02.185][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.186][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.187][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:02.188][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:02.188][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.189][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.191][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-17 19:28:02.193][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.194][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 19:28:02.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:02.198][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.199][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.200][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.203][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 19:28:02.203][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:02.204][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.205][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-17 19:28:02.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:02.207][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.208][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:02.209][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.211][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:02.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:02.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:02.215][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:02.216][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:02.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:02.218][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:02.219][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.220][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:02.222][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:02.238][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:02.240][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:02.241][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:28:02.242][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.247][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[2024-05-17 19:28:02.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.260][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[2024-05-17 19:28:02.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.285][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[2024-05-17 19:28:02.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.300][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.DEBUG[2024-05-17 19:28:02.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.346][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-17 19:28:02.353][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-17 19:28:02.356][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-17 19:28:02.358][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-17 19:28:02.361][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 19:28:02.369][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-17 19:28:02.372][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-17 19:28:02.375][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-17 19:28:02.377][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-17 19:28:02.384][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-17 19:28:02.387][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 19:28:02.389][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-17 19:28:02.392][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-17 19:28:02.399][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-17 19:28:02.401][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-17 19:28:02.404][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 19:28:02.407][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-17 19:28:02.414][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-17 19:28:02.417][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 19:28:02.419][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-17 19:28:02.421][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-17 19:28:02.426][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-17 19:28:02.434][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-17 19:28:02.437][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-17 19:28:02.439][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-17 19:28:02.442][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-17 19:28:02.457][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-17 19:28:02.462][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-17 19:28:02.464][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-17 19:28:02.473][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-17 19:28:02.475][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-17 19:28:02.478][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-17 19:28:02.480][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-17 19:28:02.482][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-17 19:28:02.491][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-17 19:28:02.493][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-17 19:28:02.495][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-17 19:28:02.497][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-17 19:28:02.507][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-17 19:28:02.510][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-17 19:28:02.512][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-17 19:28:02.515][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-17 19:28:02.517][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-17 19:28:02.520][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-17 19:28:02.522][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-17 19:28:02.524][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-17 19:28:02.535][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-17 19:28:02.539][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-17 19:28:02.542][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-17 19:28:02.544][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-17 19:28:02.556][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-17 19:28:02.558][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-17 19:28:02.560][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-17 19:28:02.563][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-17 19:28:02.588][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-17 19:28:02.591][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-17 19:28:02.593][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-17 19:28:02.597][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-17 19:28:02.599][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-17 19:28:02.602][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-17 19:28:02.604][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-17 19:28:02.606][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-17 19:28:02.616][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-17 19:28:02.620][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-17 19:28:02.622][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-17 19:28:02.631][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-17 19:28:02.635][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 19:28:02.638][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 19:28:02.640][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-17 19:28:02.642][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-17 19:28:02.652][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-17 19:28:02.655][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-17 19:28:02.658][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-17 19:28:02.662][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-17 19:28:02.673][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-17 19:28:02.676][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-17 19:28:02.679][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-17 19:28:02.682][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-17 19:28:02.684][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-17 19:28:02.686][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-17 19:28:02.688][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-17 19:28:02.690][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-17 19:28:02.700][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-17 19:28:02.704][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-17 19:28:02.706][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-17 19:28:02.708][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:28:02.710][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.713][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.714][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[2024-05-17 19:28:02.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.723][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[2024-05-17 19:28:02.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.873][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[2024-05-17 19:28:02.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.939][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[2024-05-17 19:28:02.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:02.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:02.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:02.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:02.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:02.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:02.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:02.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:03.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:03.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:03.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:03.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:03.006][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[2024-05-17 19:28:03.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:03.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:03.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:03.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:03.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:03.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:03.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:03.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:03.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:03.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:03.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:03.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:03.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:03.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:03.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:03.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:03.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:03.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:03.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:03.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:03.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:03.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:03.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:03.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:03.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:03.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:03.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:03.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:03.048][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-17 19:28:03.054][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:28:03.056][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:03.057][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-17 19:28:03.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:03.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:03.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:03.060][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:03.062][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:03.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:03.064][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:28:03.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:03.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:03.068][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-17 19:28:03.069][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-17 19:28:03.070][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-17 19:28:03.072][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:03.073][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:28:03.073][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:28:03.074][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:03.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:03.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:03.076][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:03.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:03.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:03.084][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:03.089][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-17 19:28:03.089][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-17 19:28:03.091][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:03.092][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:03.093][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:03.095][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:03.097][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-17 19:28:03.102][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 19:28:03.115][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:28:03.117][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-17 19:28:03.121][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:28:03.123][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-17 19:28:03.124][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-17 19:28:03.125][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-17 19:28:03.127][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-17 19:28:03.128][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-17 19:28:03.130][biodb::testThat]
biodb.INFO [2024-05-17 19:28:03.131][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-05-17 19:28:03.132][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:28:03.133][biodb::testThat]
biodb.DEBUG[2024-05-17 19:28:03.142][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-05-17 19:28:03.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:28:03.149][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:28:03.151][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-05-17 19:28:03.779][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-05-17 19:28:04.444][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:28:04.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-05-17 19:28:04.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-05-17 19:28:04.530][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[2024-05-17 19:28:04.537][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:28:04.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:28:04.543][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-05-17 19:28:05.183][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-05-17 19:28:05.820][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:28:05.823][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-05-17 19:28:05.829][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-05-17 19:28:05.855][biodb::testThat]
biodb.INFO [2024-05-17 19:28:05.856][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-05-17 19:28:05.856][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:28:05.857][biodb::testThat]
biodb.INFO [2024-05-17 19:28:05.913][biodb::testThat]
biodb.INFO [2024-05-17 19:28:05.914][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-05-17 19:28:05.916][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:28:05.917][biodb::testThat]
biodb.DEBUG[2024-05-17 19:28:05.920][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-17 19:28:05.923][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:28:05.924][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:28:05.925][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-05-17 19:28:06.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-05-17 19:28:06.920][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:28:06.922][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-05-17 19:28:06.925][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-05-17 19:28:06.929][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[2024-05-17 19:28:06.933][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 19:28:06.934][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-17 19:28:06.935][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 19:28:06.961][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-17 19:28:06.968][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[2024-05-17 19:28:06.971][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:28:06.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:28:06.974][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-05-17 19:28:07.439][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-05-17 19:28:07.929][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:28:07.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-05-17 19:28:07.936][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-05-17 19:28:07.960][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-05-17 19:28:07.964][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:28:07.965][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-17 19:28:07.966][rule$waitAsNeeded] Wait 0.00751805 second(s).
biodb.TRACE[2024-05-17 19:28:08.017][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-05-17 19:28:09.259][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-05-17 19:28:13.370][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:28:13.372][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-05-17 19:28:13.384][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-05-17 19:28:14.182][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-05-17 19:28:14.185][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-17 19:28:14.186][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-17 19:28:14.187][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-05-17 19:28:15.413][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-05-17 19:28:19.100][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-17 19:28:19.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-05-17 19:28:19.241][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-05-17 19:28:19.817][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-17 19:28:19.819][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-17 19:28:19.822][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-17 19:28:19.824][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-17 19:28:19.826][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:19.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:19.831][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:19.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:19.834][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.835][FUN] Functions in observer BiodbConfig: [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 [2024-05-17 19:28:19.845][biodb::testContext]
biodb.INFO [2024-05-17 19:28:19.847][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 19:28:19.849][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-05-17 19:28:19.851][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-17 19:28:19.854][biodb::testContext]
biodb.INFO [2024-05-17 19:28:19.859][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-17 19:28:19.862][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-17 19:28:19.876][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:28:19.879][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-17 19:28:19.881][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-17 19:28:19.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.888][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-17 19:28:19.890][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-17 19:28:19.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.898][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-17 19:28:19.900][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-17 19:28:19.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.907][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-17 19:28:19.908][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-17 19:28:19.910][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-17 19:28:19.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.916][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-17 19:28:19.918][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-17 19:28:19.920][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-17 19:28:19.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.926][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-17 19:28:19.927][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-17 19:28:19.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.934][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-17 19:28:19.935][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-17 19:28:19.937][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-17 19:28:19.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.944][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-17 19:28:19.945][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-17 19:28:19.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.951][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-17 19:28:19.953][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-17 19:28:19.954][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-17 19:28:19.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.960][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-17 19:28:19.961][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-17 19:28:19.962][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-17 19:28:19.964][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-17 19:28:19.965][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-17 19:28:19.967][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-17 19:28:19.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.974][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-17 19:28:19.978][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-17 19:28:19.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.987][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-17 19:28:19.989][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-17 19:28:19.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:19.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:19.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:19.998][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-17 19:28:20.000][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-17 19:28:20.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.012][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-17 19:28:20.014][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-17 19:28:20.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.023][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-17 19:28:20.025][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-17 19:28:20.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.045][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-17 19:28:20.049][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-17 19:28:20.227][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-17 19:28:20.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.236][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-17 19:28:20.239][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-17 19:28:20.243][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-17 19:28:20.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.252][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-17 19:28:20.255][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.258][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-17 19:28:20.260][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.262][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:20.264][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.271][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.273][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.275][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.276][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:28:20.280][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:20.282][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.284][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-17 19:28:20.288][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:20.290][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.292][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:28:20.293][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:28:20.293][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 19:28:20.293][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 19:28:20.293][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 19:28:20.295][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:20.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:20.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.304][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.306][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.307][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:20.309][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:20.311][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.313][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.318][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-17 19:28:20.322][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.331][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 19:28:20.333][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:20.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.339][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.341][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.346][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 19:28:20.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:20.350][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.351][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-17 19:28:20.352][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:20.353][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.355][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.356][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:28:20.356][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:28:20.356][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-17 19:28:20.356][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-17 19:28:20.356][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-17 19:28:20.358][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:20.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.362][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.363][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:20.365][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.368][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.371][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:20.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:20.381][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.383][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.384][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-17 19:28:20.386][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.388][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-17 19:28:20.389][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:20.400][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.401][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.403][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.409][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.410][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:28:20.513][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:20.514][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.515][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-17 19:28:20.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:20.516][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.517][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.518][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.519][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:20.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.521][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:20.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.524][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.524][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.525][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:20.526][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:20.526][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.527][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.528][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-17 19:28:20.530][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.531][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-17 19:28:20.531][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:20.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.534][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.535][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.536][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-17 19:28:20.537][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:20.537][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.538][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-17 19:28:20.539][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:20.540][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.541][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.541][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.542][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:20.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:20.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.546][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.547][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.548][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:20.548][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:20.549][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.550][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.551][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:28:20.552][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.553][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[2024-05-17 19:28:20.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.585][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[2024-05-17 19:28:20.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.634][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[2024-05-17 19:28:20.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.638][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-17 19:28:20.640][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-17 19:28:20.641][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-17 19:28:20.642][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-17 19:28:20.643][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-17 19:28:20.644][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-17 19:28:20.645][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-17 19:28:20.646][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-17 19:28:20.647][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-17 19:28:20.648][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-17 19:28:20.649][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-17 19:28:20.651][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-17 19:28:20.652][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-17 19:28:20.653][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-17 19:28:20.654][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-17 19:28:20.656][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 19:28:20.657][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-17 19:28:20.658][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-17 19:28:20.659][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-17 19:28:20.660][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-17 19:28:20.662][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-17 19:28:20.663][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-17 19:28:20.664][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-17 19:28:20.665][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-17 19:28:20.666][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-17 19:28:20.667][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-17 19:28:20.668][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-17 19:28:20.669][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-17 19:28:20.671][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-17 19:28:20.672][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-17 19:28:20.674][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-17 19:28:20.675][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-17 19:28:20.676][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-17 19:28:20.677][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-17 19:28:20.678][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-17 19:28:20.679][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-17 19:28:20.680][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-17 19:28:20.681][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-17 19:28:20.683][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-17 19:28:20.685][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-17 19:28:20.687][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-17 19:28:20.688][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-17 19:28:20.689][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-17 19:28:20.690][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-17 19:28:20.691][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-17 19:28:20.692][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-17 19:28:20.694][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-17 19:28:20.695][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-17 19:28:20.696][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-17 19:28:20.698][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-17 19:28:20.699][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-17 19:28:20.700][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-17 19:28:20.701][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-17 19:28:20.702][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-17 19:28:20.703][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-17 19:28:20.704][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-17 19:28:20.706][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-17 19:28:20.707][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-17 19:28:20.708][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-17 19:28:20.709][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-17 19:28:20.711][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-17 19:28:20.712][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-17 19:28:20.713][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-17 19:28:20.714][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-17 19:28:20.715][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-17 19:28:20.716][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-17 19:28:20.718][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-17 19:28:20.720][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-17 19:28:20.721][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-17 19:28:20.722][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-17 19:28:20.723][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-17 19:28:20.724][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-17 19:28:20.725][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-17 19:28:20.726][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-17 19:28:20.727][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-17 19:28:20.728][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-17 19:28:20.729][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-17 19:28:20.730][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-17 19:28:20.732][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-17 19:28:20.734][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-17 19:28:20.735][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-17 19:28:20.736][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-17 19:28:20.737][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-17 19:28:20.738][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-17 19:28:20.739][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-17 19:28:20.740][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-17 19:28:20.741][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.754][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.766][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[2024-05-17 19:28:20.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.776][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[2024-05-17 19:28:20.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.857][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[2024-05-17 19:28:20.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-17 19:28:20.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-17 19:28:20.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:20.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:20.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:20.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:20.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:20.866][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[2024-05-17 19:28:20.871][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-17 19:28:20.873][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:28:20.875][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.876][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.877][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.877][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-17 19:28:20.878][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.879][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.880][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.880][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.881][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-17 19:28:20.882][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-17 19:28:20.883][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.883][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-17 19:28:20.884][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-17 19:28:20.885][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-17 19:28:20.886][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-17 19:28:20.887][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-17 19:28:20.887][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-17 19:28:20.888][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-17 19:28:20.888][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.889][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.890][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-17 19:28:20.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-17 19:28:20.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-17 19:28:20.892][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-17 19:28:20.892][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-17 19:28:20.892][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-17 19:28:20.893][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-17 19:28:20.894][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-17 19:28:20.905][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-17 19:28:20.906][self$setPropertyValue]
biodb.DEBUG[2024-05-17 19:28:20.907][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-17 19:28:20.908][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-17 19:28:20.910][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:28:20.911][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-17 19:28:20.912][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-17 19:28:20.913][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-17 19:28:20.914][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-17 19:28:20.914][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-17 19:28:20.915][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-17 19:28:20.916][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-17 19:28:20.917][biodb::testThat]
biodb.INFO [2024-05-17 19:28:20.918][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-05-17 19:28:20.919][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-17 19:28:20.920][biodb::testThat]
biodb.DEBUG[2024-05-17 19:28:20.922][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[2024-05-17 19:28:20.935][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-17 19:28:20.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-17 19:28:20.937][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-17 19:28:23.425][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-05-17 19:28:25.910][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-05-17 19:28:25.914][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-17 19:28:25.917][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-05-17 19:28:25.923][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-17 19:28:25.927][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[2024-05-17 19:28:25.929][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-17 19:28:25.931][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-17 19:28:25.933][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-17 19:28:25.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:28:25.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:25.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:25.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:25.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:25.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:25.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:28:25.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:25.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:25.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:25.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:25.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:25.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:25.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:25.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:25.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:25.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:25.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:25.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.013][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:28:26.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:28:26.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.024][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:28:26.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:28:26.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.030][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.039][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.079][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:28:26.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.087][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:28:26.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.114][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.133][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:28:26.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.141][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-17 19:28:26.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.170][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:28:26.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.218][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.227][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.238][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.252][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:28:26.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:28:26.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:26.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:26.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:26.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:26.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:26.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:28:26.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.344][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:28:26.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-17 19:28:26.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.349][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:28:26.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-17 19:28:26.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.354][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.358][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.363][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.379][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.386][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:28:26.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.398][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-17 19:28:26.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.402][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.407][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.431][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:28:26.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.437][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-17 19:28:26.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.488][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-17 19:28:26.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.494][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.500][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-17 19:28:26.561][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-05-17 19:28:26.563][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-17 19:28:26.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:28:26.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:26.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:26.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:26.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:26.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:26.575][FUN] Functions in observer BiodbConfig: [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[2024-05-17 19:28:26.578][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:28:26.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:28:26.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.583][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:28:26.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:28:26.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-17 19:28:26.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-17 19:28:26.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.600][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-17 19:28:26.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-17 19:28:26.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.604][private$selectFields] Fields none
biodb.TRACE[2024-05-17 19:28:26.605][private$selectFields]
biodb.TRACE[2024-05-17 19:28:26.606][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-17 19:28:26.608][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:28:26.609][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:28:26.610][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.611][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.612][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.613][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.614][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.616][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.619][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.620][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.621][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.622][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.623][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.625][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.626][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.626][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.628][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.629][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.631][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.634][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.635][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.636][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.638][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.639][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.641][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.644][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.645][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.646][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.649][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.651][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.654][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.655][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.657][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.659][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.660][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.672][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.675][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.676][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.678][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.681][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.682][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.683][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.686][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.687][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.690][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.690][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.691][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.694][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.694][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:28:26.695][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:28:26.697][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.699][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.700][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.701][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.702][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.704][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.705][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.707][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.708][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.709][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.711][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.713][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.717][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.718][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.720][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.721][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.723][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.725][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.726][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.728][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.731][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.732][private$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[2024-05-17 19:28:26.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.776][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.782][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.788][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.799][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.804][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.861][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.880][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.883][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.887][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.903][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-05-17 19:28:26.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-17 19:28:26.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:26.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:26.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:26.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:26.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:26.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-17 19:28:26.917][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:28:26.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:28:26.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.922][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-17 19:28:26.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-17 19:28:26.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-17 19:28:26.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-17 19:28:26.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.932][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-17 19:28:26.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-17 19:28:26.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.937][private$selectFields] Fields none
biodb.TRACE[2024-05-17 19:28:26.938][private$selectFields]
biodb.TRACE[2024-05-17 19:28:26.939][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-17 19:28:26.940][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-17 19:28:26.942][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:28:26.943][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.945][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.947][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.949][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.950][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.953][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.954][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.955][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.956][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.957][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.958][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.960][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.960][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.961][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.964][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.965][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.966][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:26.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.968][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.968][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:26.969][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:26.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.971][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.972][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.972][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:26.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.974][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.975][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:26.976][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:26.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.979][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.979][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:26.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.984][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.985][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:26.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.987][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.988][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.989][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:26.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.991][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.992][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.994][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:26.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:26.996][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:26.998][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:26.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:27.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.003][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:27.004][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:27.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.006][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.006][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.008][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.010][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.011][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:28:27.012][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-17 19:28:27.014][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:27.015][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:27.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.018][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.019][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:27.021][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:27.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.023][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.025][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:27.026][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:27.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.028][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.030][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:27.031][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:27.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.033][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.035][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:27.036][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:27.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.038][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.039][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:27.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:27.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.042][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.044][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:27.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:27.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.049][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.050][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.052][ef$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.054][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-05-17 19:28:27.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:27.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:27.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:27.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:27.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-17 19:28:27.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-17 19:28:27.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:27.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:27.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:27.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:27.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-17 19:28:27.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-17 19:28:27.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.083][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:27.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:27.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.088][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:27.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:27.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.093][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:27.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-17 19:28:27.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:27.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:27.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.104][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:27.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:27.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.109][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:27.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-17 19:28:27.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:27.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:27.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:27.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:27.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:27.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-17 19:28:27.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:27.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:27.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.135][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:27.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:27.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-17 19:28:27.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-17 19:28:27.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:27.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:27.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:27.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:27.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-17 19:28:27.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-17 19:28:27.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.179][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.185][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.189][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-17 19:28:27.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-17 19:28:27.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-17 19:28:27.201][private$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[2024-05-17 19:28:27.202][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-05-17 19:28:27.203][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-05-17 19:28:27.215][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-17 19:28:27.217][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-17 19:28:27.219][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-17 19:28:27.220][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-17 19:28:27.221][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-17 19:28:27.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-17 19:28:27.224][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-17 19:28:27.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-17 19:28:27.226][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-17 19:28:27.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]

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

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

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

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

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.4000.9333.403
LipidmapsStructureEntry0.3650.0200.403