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This page was generated on 2024-05-09 11:40:36 -0400 (Thu, 09 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4748
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4484
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4514
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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: 2024-05-08 14:00:19 -0400 (Wed, 08 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    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for biodbLipidmaps on kunpeng2


To the developers/maintainers of the biodbLipidmaps package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-05-09 05:17:28 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 05:24:00 -0000 (Thu, 09 May 2024)
EllapsedTime: 392.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 1.084  0.056   5.345
* 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 166 ]
  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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log’
for details.

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 [2024-05-09 05:19:48.645][biodb::testContext]
biodb.INFO [2024-05-09 05:19:48.648][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-09 05:19:48.649][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-09 05:19:48.651][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-09 05:19:48.652][biodb::testContext]
biodb.INFO [2024-05-09 05:19:48.661][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-09 05:19:48.663][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-09 05:19:48.673][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:19:48.674][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-09 05:19:48.676][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-09 05:19:48.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.682][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-09 05:19:48.710][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-09 05:19:48.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.716][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-09 05:19:48.718][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-09 05:19:48.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.724][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-09 05:19:48.725][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-09 05:19:48.727][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-09 05:19:48.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.732][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-09 05:19:48.734][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-09 05:19:48.736][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-09 05:19:48.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.741][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-09 05:19:48.743][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-09 05:19:48.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.749][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-09 05:19:48.750][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-09 05:19:48.752][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-09 05:19:48.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.758][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-09 05:19:48.759][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-09 05:19:48.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.765][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-09 05:19:48.767][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-09 05:19:48.769][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-09 05:19:48.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.775][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-09 05:19:48.776][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-09 05:19:48.778][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-09 05:19:48.780][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-09 05:19:48.781][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-09 05:19:48.783][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-09 05:19:48.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.788][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-09 05:19:48.790][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-09 05:19:48.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.795][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-09 05:19:48.797][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-09 05:19:48.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.801][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[2024-05-09 05:19:48.802][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-09 05:19:48.804][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-09 05:19:48.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.810][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-09 05:19:48.811][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-09 05:19:48.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.817][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-09 05:19:48.818][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-09 05:19:48.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.824][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-09 05:19:48.825][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-09 05:19:48.831][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-09 05:19:48.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.835][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.DEBUG[2024-05-09 05:19:48.836][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-09 05:19:48.838][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-09 05:19:48.839][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-09 05:19:48.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:48.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:48.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:48.848][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-09 05:19:48.898][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:48.934][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-09 05:19:48.936][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:48.937][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:19:48.939][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:48.940][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:19:48.942][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:48.943][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:19:48.944][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:19:48.946][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:19:48.947][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:48.949][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-09 05:19:48.950][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:19:48.951][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:48.953][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:48.954][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:19:48.954][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:19:48.954][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-09 05:19:48.954][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-09 05:19:48.954][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-09 05:19:48.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:19:48.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:48.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:48.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:19:48.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:48.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:48.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:19:48.965][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:48.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:19:48.968][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:19:48.969][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:48.970][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:48.972][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-09 05:19:48.975][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:48.976][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-09 05:19:48.978][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:48.979][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:19:48.980][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:48.982][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:19:48.983][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:48.985][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:19:48.986][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-09 05:19:48.987][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:19:48.989][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:48.990][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-09 05:19:48.992][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:19:48.993][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:48.994][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:48.996][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:19:48.996][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:19:48.996][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-09 05:19:48.996][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-09 05:19:48.996][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-09 05:19:48.997][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:19:48.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:49.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:49.001][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:19:49.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:49.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:49.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.007][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.008][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:19:49.009][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:19:49.010][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.012][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.014][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-09 05:19:49.016][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.018][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-09 05:19:49.019][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.020][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:19:49.022][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.023][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.028][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:19:49.029][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:19:49.031][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.032][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-09 05:19:49.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:19:49.035][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.036][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.038][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.039][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:19:49.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:49.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:49.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:19:49.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:49.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:49.048][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.049][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:19:49.052][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:19:49.053][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.055][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.056][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-09 05:19:49.059][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.061][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-09 05:19:49.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:19:49.065][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.067][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.068][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.070][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.071][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-09 05:19:49.073][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:19:49.074][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.076][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-09 05:19:49.077][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:19:49.078][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.080][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.081][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:19:49.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:49.085][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:49.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:19:49.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:49.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:49.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.092][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:19:49.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:19:49.096][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.098][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.103][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:19:49.105][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.203][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[2024-05-09 05:19:49.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.209][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[2024-05-09 05:19:49.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.217][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-09 05:19:49.223][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-09 05:19:49.225][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-09 05:19:49.227][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-09 05:19:49.229][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-09 05:19:49.231][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-09 05:19:49.233][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-09 05:19:49.235][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-09 05:19:49.237][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-09 05:19:49.239][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-09 05:19:49.241][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-09 05:19:49.243][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-09 05:19:49.245][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-09 05:19:49.247][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-09 05:19:49.249][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-09 05:19:49.251][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-09 05:19:49.253][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-09 05:19:49.255][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-09 05:19:49.257][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-09 05:19:49.259][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-09 05:19:49.261][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-09 05:19:49.263][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-09 05:19:49.265][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-09 05:19:49.267][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-09 05:19:49.269][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-09 05:19:49.271][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-09 05:19:49.273][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-09 05:19:49.275][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-09 05:19:49.277][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-09 05:19:49.279][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-09 05:19:49.281][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-09 05:19:49.283][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-09 05:19:49.285][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-09 05:19:49.287][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-09 05:19:49.288][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-09 05:19:49.290][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-09 05:19:49.292][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-09 05:19:49.302][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-09 05:19:49.304][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-09 05:19:49.306][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-09 05:19:49.308][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-09 05:19:49.310][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-09 05:19:49.312][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-09 05:19:49.314][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-09 05:19:49.316][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-09 05:19:49.318][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-09 05:19:49.320][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-09 05:19:49.322][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-09 05:19:49.324][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-09 05:19:49.326][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-09 05:19:49.328][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-09 05:19:49.330][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-09 05:19:49.331][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-09 05:19:49.333][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-09 05:19:49.335][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-09 05:19:49.337][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-09 05:19:49.339][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-09 05:19:49.341][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-09 05:19:49.343][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-09 05:19:49.345][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-09 05:19:49.347][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-09 05:19:49.349][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-09 05:19:49.351][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-09 05:19:49.353][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-09 05:19:49.355][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-09 05:19:49.357][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-09 05:19:49.359][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-09 05:19:49.361][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-09 05:19:49.363][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-09 05:19:49.365][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-09 05:19:49.367][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-09 05:19:49.369][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-09 05:19:49.371][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-09 05:19:49.373][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-09 05:19:49.375][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-09 05:19:49.377][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-09 05:19:49.379][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-09 05:19:49.381][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-09 05:19:49.383][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-09 05:19:49.385][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-09 05:19:49.387][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-09 05:19:49.389][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-09 05:19:49.391][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-09 05:19:49.400][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-09 05:19:49.402][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-09 05:19:49.406][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:19:49.407][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.410][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.442][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.DEBUG[2024-05-09 05:19:49.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:19:49.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:19:49.565][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-09 05:19:49.579][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:19:49.581][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.583][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.584][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:19:49.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.590][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.591][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.593][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:19:49.594][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:19:49.596][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.597][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-09 05:19:49.599][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-09 05:19:49.600][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-09 05:19:49.602][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-09 05:19:49.603][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:19:49.603][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:19:49.605][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:19:49.606][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:49.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:49.609][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:19:49.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:19:49.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:19:49.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:19:49.614][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-09 05:19:49.614][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-09 05:19:49.616][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:19:49.617][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:19:49.618][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-09 05:19:49.620][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:19:49.628][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-09 05:19:49.631][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-09 05:19:49.671][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:19:49.672][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-09 05:19:49.677][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:19:49.683][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-09 05:19:49.688][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-09 05:19:49.689][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-09 05:19:49.691][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-09 05:19:49.693][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-09 05:19:49.704][biodb::testThat]
biodb.INFO [2024-05-09 05:19:49.706][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-09 05:19:49.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:49.708][biodb::testThat]
biodb.TRACE[2024-05-09 05:19:49.713][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-05-09 05:19:49.716][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-09 05:19:49.720][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-09 05:19:49.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:19:49.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:49.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:49.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:49.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:49.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:49.753][FUN] Functions in observer BiodbConfig: [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[2024-05-09 05:19:49.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:49.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:49.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:49.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:19:49.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:19:49.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:19:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:19:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.807][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:19:49.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:19:49.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.813][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:49.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:49.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.855][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:49.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:49.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.861][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:49.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:49.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:49.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:49.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:19:49.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:49.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.878][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:19:49.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:49.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:49.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:49.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.889][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:49.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:49.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:49.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:49.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.906][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:19:49.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.912][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-09 05:19:49.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:49.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.930][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:19:49.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:49.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:49.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:49.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:49.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:49.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.058][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.069][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:19:50.107][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-09 05:19:50.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:19:50.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:19:50.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.116][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:19:50.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:19:50.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.122][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-09 05:19:50.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-09 05:19:50.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.127][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-09 05:19:50.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-09 05:19:50.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.173][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.220][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.226][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.232][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.264][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.266][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.268][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.302][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.304][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.306][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.360][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.366][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.371][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.376][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.378][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.381][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.382][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.398][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:50.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:50.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.404][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:50.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:50.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.410][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:50.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:50.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.415][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:50.417][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:50.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.419][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:50.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.454][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.456][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.458][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.482][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.487][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.493][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.495][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.499][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.516][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.517][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.520][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.527][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.528][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.538][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:50.539][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:50.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.542][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.548][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.550][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.552][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.559][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.560][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.563][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.569][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.571][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.573][ef$get] fields variable is a list.
biodb.INFO [2024-05-09 05:19:50.584][biodb::testThat]
biodb.INFO [2024-05-09 05:19:50.585][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-09 05:19:50.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:50.588][biodb::testThat]
biodb.DEBUG[2024-05-09 05:19:50.607][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-05-09 05:19:50.616][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-09 05:19:50.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-05-09 05:19:50.622][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-09 05:19:50.624][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-05-09 05:19:50.626][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-09 05:19:50.661][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-09 05:19:50.662][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-09 05:19:50.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:19:50.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:19:50.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:19:50.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:19:50.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:19:50.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:19:50.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:19:50.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:19:50.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:19:50.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:19:50.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:19:50.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:19:50.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:19:50.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.722][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:19:50.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:19:50.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.728][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.734][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:19:50.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.740][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:19:50.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.752][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:19:50.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.758][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:19:50.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:50.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.764][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:50.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:50.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.770][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:19:50.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:19:50.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.787][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:19:50.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.793][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-09 05:19:50.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.810][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:19:50.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.846][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.852][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.863][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:19:50.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:19:50.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:19:50.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:19:50.905][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-09 05:19:50.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-09 05:19:50.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-09 05:19:50.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-09 05:19:50.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-09 05:19:50.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:50.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-09 05:19:50.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-09 05:19:50.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-09 05:19:50.933][biodb::testThat]
biodb.INFO [2024-05-09 05:19:50.935][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-09 05:19:50.936][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:50.938][biodb::testThat]
biodb.TRACE[2024-05-09 05:19:50.943][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.944][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.947][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:19:50.949][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-05-09 05:19:50.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:50.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:50.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:50.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:51.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:51.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:51.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:51.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:51.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:51.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:51.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:51.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:19:51.015][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-09 05:19:51.022][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[2024-05-09 05:19:51.052][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:19:51.053][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:19:51.055][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-05-09 05:19:53.268][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-05-09 05:19:55.562][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:19:55.575][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-05-09 05:19:55.615][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-05-09 05:19:55.621][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-05-09 05:19:55.653][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:55.656][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:55.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:55.660][ef$get] fields variable is a list.
biodb.INFO [2024-05-09 05:19:55.669][biodb::testThat]
biodb.INFO [2024-05-09 05:19:55.671][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-09 05:19:55.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:55.674][biodb::testThat]
biodb.TRACE[2024-05-09 05:19:55.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:55.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:55.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:55.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:55.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:55.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:55.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:55.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:55.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:55.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:55.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:55.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:19:56.056][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-09 05:19:56.060][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-09 05:19:56.083][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-09 05:19:56.085][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-09 05:19:56.087][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-05-09 05:19:56.116][biodb::testThat]
biodb.INFO [2024-05-09 05:19:56.117][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-09 05:19:56.119][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:56.120][biodb::testThat]
biodb.TRACE[2024-05-09 05:19:56.149][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:19:56.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:19:56.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:56.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:56.155][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:19:56.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:19:56.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:56.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:56.160][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-09 05:19:56.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-09 05:19:56.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:56.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:56.166][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-09 05:19:56.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-09 05:19:56.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:56.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:56.230][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:19:56.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:19:56.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:56.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:56.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:19:56.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:19:56.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:56.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:56.241][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-09 05:19:56.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-09 05:19:56.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:56.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:56.246][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-09 05:19:56.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-09 05:19:56.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:56.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-09 05:19:56.258][biodb::testThat]
biodb.INFO [2024-05-09 05:19:56.260][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-09 05:19:56.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:56.262][biodb::testThat]
biodb.INFO [2024-05-09 05:19:56.273][biodb::testThat]
biodb.INFO [2024-05-09 05:19:56.274][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-09 05:19:56.275][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:56.277][biodb::testThat]
biodb.INFO [2024-05-09 05:19:56.287][biodb::testThat]
biodb.INFO [2024-05-09 05:19:56.288][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-09 05:19:56.289][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:56.291][biodb::testThat]
biodb.DEBUG[2024-05-09 05:19:56.296][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-05-09 05:19:58.100][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-05-09 05:19:59.246][biodb::testThat]
biodb.INFO [2024-05-09 05:19:59.247][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-09 05:19:59.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:59.250][biodb::testThat]
biodb.TRACE[2024-05-09 05:19:59.257][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:59.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:59.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.262][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.263][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.264][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.267][ef$get] fields variable is a list.
biodb.INFO [2024-05-09 05:19:59.270][biodb::testThat]
biodb.INFO [2024-05-09 05:19:59.271][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-09 05:19:59.272][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:19:59.286][biodb::testThat]
biodb.TRACE[2024-05-09 05:19:59.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:59.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:59.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:59.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:59.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:19:59.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:19:59.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:19:59.427][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-09 05:19:59.431][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-09 05:19:59.433][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-09 05:19:59.435][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-09 05:19:59.437][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-09 05:19:59.522][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-09 05:19:59.526][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-09 05:19:59.528][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-09 05:19:59.539][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-09 05:19:59.542][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-05-09 05:19:59.560][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-09 05:19:59.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-09 05:19:59.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-09 05:19:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-09 05:19:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:19:59.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:19:59.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:19:59.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:19:59.622][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-09 05:19:59.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:19:59.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:19:59.670][private$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[2024-05-09 05:20:04.475][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[2024-05-09 05:20:37.349][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:20:37.353][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-05-09 05:20:37.385][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-05-09 05:20:38.599][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[2024-05-09 05:20:38.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:20:38.606][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:20:38.609][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-09 05:20:39.922][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-05-09 05:20:41.271][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:20:41.274][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-05-09 05:20:41.279][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-05-09 05:20:41.308][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-05-09 05:20:41.314][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:20:41.315][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:20:41.318][private$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[2024-05-09 05:20:42.612][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[2024-05-09 05:20:44.103][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:20:44.105][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-05-09 05:20:44.111][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-05-09 05:20:44.134][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-09 05:20:44.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-09 05:20:44.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:20:44.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-09 05:20:44.149][biodb::testThat]
biodb.INFO [2024-05-09 05:20:44.151][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-09 05:20:44.152][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:20:44.153][biodb::testThat]
biodb.TRACE[2024-05-09 05:20:44.157][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-09 05:20:44.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-09 05:20:44.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:20:44.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:20:44.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-09 05:20:44.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-09 05:20:44.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:20:44.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:20:44.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:20:44.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:20:44.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:20:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:20:44.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:20:44.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:20:44.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:20:44.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:20:44.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:20:44.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:20:44.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:20:44.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:20:44.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:20:44.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:20:44.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:20:44.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:20:44.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:20:44.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:20:44.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:20:44.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:20:44.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:20:44.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:20:44.209][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[2024-05-09 05:20:44.213][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[2024-05-09 05:20:44.218][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:20:44.220][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:20:44.222][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-05-09 05:20:48.842][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-05-09 05:20:59.176][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:20:59.178][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-05-09 05:20:59.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-05-09 05:21:00.360][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-05-09 05:21:00.432][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-09 05:21:00.435][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-05-09 05:21:00.438][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-09 05:21:00.439][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-09 05:21:00.441][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-09 05:21:00.443][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-09 05:21:00.445][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-09 05:21:00.446][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-09 05:21:00.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:00.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:00.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:00.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:00.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:00.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:00.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:21:00.487][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-05-09 05:21:00.492][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:00.493][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:00.495][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-09 05:21:01.813][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-05-09 05:21:03.133][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:21:03.136][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-05-09 05:21:03.141][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-05-09 05:21:03.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:03.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:03.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:03.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:03.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:03.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:03.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:21:03.160][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-05-09 05:21:03.164][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:03.166][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:03.167][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-05-09 05:21:05.756][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-05-09 05:21:07.073][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:21:07.076][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-05-09 05:21:07.081][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-05-09 05:21:07.085][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-05-09 05:21:07.087][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-09 05:21:07.089][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-09 05:21:07.091][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-09 05:21:07.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:07.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:07.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:07.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:07.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:07.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:07.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:21:07.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:21:07.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:21:07.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:21:07.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:21:07.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:21:07.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.173][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:21:07.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:21:07.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.179][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:21:07.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:21:07.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.186][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:21:07.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:21:07.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:21:07.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:21:07.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.199][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:21:07.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:21:07.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.207][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:21:07.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:21:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.219][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:21:07.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:21:07.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.226][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:21:07.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:21:07.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:21:07.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:21:07.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.245][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:21:07.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.251][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-09 05:21:07.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:21:07.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:21:07.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.268][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:21:07.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.274][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.291][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:21:07.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:07.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:07.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:07.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:07.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:07.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:07.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:07.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:21:07.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:21:07.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.368][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:21:07.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:21:07.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.373][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:21:07.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:21:07.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.379][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:21:07.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:21:07.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.384][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:21:07.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:21:07.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.390][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:21:07.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:21:07.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.395][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:21:07.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:21:07.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.401][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:21:07.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.407][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:21:07.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:21:07.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:21:07.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.418][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:21:07.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:21:07.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:21:07.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:21:07.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.434][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:21:07.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.440][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-09 05:21:07.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:21:07.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:21:07.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.456][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:21:07.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:21:07.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.462][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.467][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.478][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:07.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:07.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:21:07.533][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-05-09 05:21:07.546][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-09 05:21:07.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:07.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:07.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:07.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:07.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:07.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:07.579][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.TRACE[2024-05-09 05:21:07.581][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.586][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.592][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.593][private$selectFields]
biodb.TRACE[2024-05-09 05:21:07.594][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:07.595][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:07.597][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.598][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.600][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.602][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.604][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.605][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.608][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.609][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.611][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.612][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.613][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.616][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.617][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:07.619][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.624][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.630][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.648][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-09 05:21:07.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:07.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:07.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:07.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:07.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:07.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:07.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:07.664][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.669][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.674][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.676][private$selectFields]
biodb.TRACE[2024-05-09 05:21:07.677][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:07.678][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:07.680][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.681][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.682][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.686][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.688][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.690][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.692][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.693][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.694][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.696][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.698][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.700][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:07.701][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.706][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.718][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-09 05:21:07.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:07.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:07.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:07.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:07.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:07.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:07.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:07.733][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.744][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.746][private$selectFields]
biodb.TRACE[2024-05-09 05:21:07.747][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:07.748][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:07.750][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.751][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.753][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.755][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.757][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.758][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.761][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.762][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.782][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:07.783][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.785][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.787][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.789][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:07.790][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.796][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.801][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:07.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.807][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-09 05:21:07.809][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-09 05:21:07.810][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-09 05:21:07.823][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-09 05:21:07.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-09 05:21:07.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-09 05:21:07.833][biodb::testThat]
biodb.INFO [2024-05-09 05:21:07.834][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-09 05:21:07.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:21:07.837][biodb::testThat]
biodb.TRACE[2024-05-09 05:21:07.841][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-09 05:21:07.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-09 05:21:07.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-09 05:21:07.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-09 05:21:07.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:07.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:07.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:07.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:21:07.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:07.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:07.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:07.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:07.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:07.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:07.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:21:07.989][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[2024-05-09 05:21:07.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:07.995][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:07.998][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-05-09 05:21:12.757][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-05-09 05:21:23.436][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:21:23.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-05-09 05:21:23.470][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-05-09 05:21:24.906][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-09 05:21:24.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:24.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:24.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:24.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:24.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:24.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:24.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:24.972][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:24.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:24.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:24.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:24.977][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:24.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:24.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:24.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.012][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.014][private$selectFields]
biodb.TRACE[2024-05-09 05:21:25.015][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:25.017][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:25.018][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.019][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.021][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.023][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.025][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.026][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.029][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.030][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.045][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.047][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.048][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.051][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.052][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:25.053][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.058][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.069][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-09 05:21:25.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:25.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:25.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:25.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:25.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:25.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:25.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:25.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.095][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.096][private$selectFields]
biodb.TRACE[2024-05-09 05:21:25.097][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:25.098][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:25.099][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.101][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.102][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.105][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.106][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.107][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.110][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.111][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.112][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.114][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.115][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.119][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:25.121][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.126][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.131][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.137][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-09 05:21:25.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:25.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:25.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:25.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:25.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:25.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:25.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:25.153][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.158][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.163][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.164][private$selectFields]
biodb.TRACE[2024-05-09 05:21:25.166][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:25.167][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:25.168][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.169][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.171][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.173][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.174][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.176][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.178][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.180][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.181][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:25.182][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.184][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.186][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.188][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:25.189][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.195][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.201][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:25.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.208][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-09 05:21:25.209][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-09 05:21:25.210][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-09 05:21:25.223][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-09 05:21:25.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-09 05:21:25.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-09 05:21:25.234][biodb::testThat]
biodb.INFO [2024-05-09 05:21:25.235][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-09 05:21:25.237][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:21:25.238][biodb::testThat]
biodb.TRACE[2024-05-09 05:21:25.242][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-09 05:21:25.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-09 05:21:25.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-09 05:21:25.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-09 05:21:25.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:25.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:25.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:25.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:25.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:25.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:25.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:25.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:25.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:21:25.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:25.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:21:25.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:25.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:25.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:25.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:25.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:25.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:25.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:21:25.303][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-09 05:21:25.308][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-09 05:21:25.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-09 05:21:25.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-09 05:21:25.404][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-09 05:21:26.698][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-09 05:21:26.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:26.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:26.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:26.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:26.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:26.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:26.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:26.715][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.720][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.726][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.727][private$selectFields]
biodb.TRACE[2024-05-09 05:21:26.728][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:26.730][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:26.731][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.732][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.734][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.736][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.738][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.739][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.742][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.743][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.744][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.746][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.747][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.750][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.751][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:26.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.758][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.763][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.769][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-09 05:21:26.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:26.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:26.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:26.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:26.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:26.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:26.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:26.785][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.790][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.796][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.797][private$selectFields]
biodb.TRACE[2024-05-09 05:21:26.798][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:26.799][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:26.801][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.802][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.803][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.806][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.807][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.809][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.811][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.813][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.814][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.815][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.817][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.819][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.821][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:26.822][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.827][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.833][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.839][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-09 05:21:26.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:26.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:26.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:26.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:26.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:26.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:26.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:21:26.855][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.860][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.866][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.867][private$selectFields]
biodb.TRACE[2024-05-09 05:21:26.868][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-09 05:21:26.870][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:21:26.871][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.872][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.874][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.876][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.878][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.879][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.882][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.883][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.884][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:21:26.886][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.887][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.890][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.891][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-09 05:21:26.892][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.898][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.903][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:26.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:26.908][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-09 05:21:26.910][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-09 05:21:26.911][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-09 05:21:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-09 05:21:26.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-09 05:21:26.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:26.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-09 05:21:26.943][biodb::testThat]
biodb.INFO [2024-05-09 05:21:26.945][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-09 05:21:26.946][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:21:26.947][biodb::testThat]
biodb.DEBUG[2024-05-09 05:21:26.949][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-09 05:21:26.950][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-09 05:21:26.953][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-09 05:21:26.954][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-09 05:21:26.956][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-09 05:21:26.957][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-09 05:21:26.958][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-09 05:21:26.959][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-09 05:21:26.961][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-09 05:21:26.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:26.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:26.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:26.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:26.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:26.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:26.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:21:26.993][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-05-09 05:21:26.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:26.997][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:26.999][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:28.335][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:28.336][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:28.337][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:28.339][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:29.689][private$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[2024-05-09 05:21:29.691][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:29.692][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:29.694][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:31.019][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:31.021][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:31.022][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:31.023][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:32.380][private$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[2024-05-09 05:21:32.382][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:32.383][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:32.385][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:33.710][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:33.711][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:33.712][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:33.714][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:35.070][private$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[2024-05-09 05:21:35.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:35.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:35.074][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:36.364][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:36.365][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:36.366][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:36.368][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:37.757][private$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[2024-05-09 05:21:37.758][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:37.759][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:37.761][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:39.112][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:39.113][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:39.115][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:39.116][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:40.466][private$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[2024-05-09 05:21:40.467][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:40.469][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:40.470][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:41.796][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:41.797][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:41.798][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:41.799][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:43.155][private$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[2024-05-09 05:21:43.157][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:43.158][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:43.160][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:44.437][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:44.438][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:44.440][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:44.441][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:45.813][private$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[2024-05-09 05:21:45.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:45.816][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:45.818][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:47.005][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:47.007][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:47.008][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:47.009][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:48.345][private$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[2024-05-09 05:21:48.346][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:48.348][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:48.349][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:49.592][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:49.594][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:49.595][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:49.596][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:50.969][private$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[2024-05-09 05:21:50.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:50.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:50.974][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-09 05:21:52.255][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:52.256][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:52.258][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:21:52.259][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-09 05:21:53.605][private$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[2024-05-09 05:21:53.608][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-05-09 05:21:53.610][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-09 05:21:53.612][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-09 05:21:53.613][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-09 05:21:53.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:53.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:53.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:53.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:53.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:53.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:53.628][FUN] Functions in observer BiodbConfig: [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[2024-05-09 05:21:53.630][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:53.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:53.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:53.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:53.635][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:53.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:21:53.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:53.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:53.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:53.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:53.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:53.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:53.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:53.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:53.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:53.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:53.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:53.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:53.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:53.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:21:53.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:21:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:21:53.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:21:53.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:21:53.749][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-09 05:21:53.750][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-09 05:21:53.760][biodb::testThat]
biodb.INFO [2024-05-09 05:21:53.762][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-09 05:21:53.763][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:21:53.764][biodb::testThat]
biodb.DEBUG[2024-05-09 05:21:53.775][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-05-09 05:21:53.777][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-05-09 05:21:53.779][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-09 05:21:53.782][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-05-09 05:21:53.783][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-09 05:21:53.785][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-09 05:21:53.787][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-09 05:21:53.788][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-09 05:21:53.790][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-09 05:21:53.792][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-09 05:21:53.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:21:53.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:21:53.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:21:53.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:21:53.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:21:53.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:21:53.811][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[2024-05-09 05:21:53.812][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-05-09 05:21:53.816][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:53.818][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:53.820][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:21:55.057][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:55.058][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:55.060][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[2024-05-09 05:21:55.061][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:21:56.407][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:21:56.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:56.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:56.412][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:21:57.632][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:21:57.633][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:21:57.636][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[2024-05-09 05:21:57.637][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:21:58.993][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:21:58.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:21:58.996][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:21:58.997][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:22:04.128][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:04.129][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:04.131][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[2024-05-09 05:22:04.132][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:22:05.470][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:22:05.472][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:05.473][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:05.475][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:22:06.748][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:06.750][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:06.751][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[2024-05-09 05:22:06.752][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:22:09.338][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:22:09.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:09.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:09.343][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:22:10.581][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:10.582][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:10.584][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[2024-05-09 05:22:10.585][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:22:11.958][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:22:11.960][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:11.961][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:11.963][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:22:13.236][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:13.238][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:13.239][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[2024-05-09 05:22:13.240][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:22:14.591][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:22:14.593][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:14.594][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:14.595][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:22:15.828][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:15.830][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:15.831][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[2024-05-09 05:22:15.833][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:22:17.185][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:22:17.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:17.188][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:17.190][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:22:18.424][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:18.425][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:18.426][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[2024-05-09 05:22:18.428][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:22:19.766][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:22:19.767][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:19.768][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:19.770][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:22:21.065][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:21.066][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:21.068][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[2024-05-09 05:22:21.069][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:22:22.442][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:22:22.444][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:22.446][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:22.447][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-09 05:22:23.734][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:23.735][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:23.737][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[2024-05-09 05:22:23.738][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-09 05:22:25.111][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-09 05:22:25.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:22:25.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:22:25.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:22:25.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:22:25.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:22:25.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:22:25.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:22:25.128][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-05-09 05:22:25.131][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:25.133][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:25.135][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:26.377][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:26.378][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:26.379][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:26.381][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:27.753][private$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[2024-05-09 05:22:27.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:27.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:27.758][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:28.997][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:28.999][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:29.000][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:29.001][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:30.347][private$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[2024-05-09 05:22:30.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:30.350][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:30.351][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:31.606][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:31.607][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:31.609][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:31.610][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:32.980][private$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[2024-05-09 05:22:32.982][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:32.983][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:32.985][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:34.271][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:34.273][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:34.274][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:34.275][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:35.489][private$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[2024-05-09 05:22:35.491][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:35.492][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:35.494][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:36.760][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:36.761][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:36.762][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:36.764][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:38.112][private$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[2024-05-09 05:22:38.113][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:38.115][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:38.116][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:39.369][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:39.370][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:39.372][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:39.374][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:40.725][private$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[2024-05-09 05:22:40.726][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:40.728][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:40.730][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:42.021][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:42.022][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:42.024][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:42.025][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:43.398][private$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[2024-05-09 05:22:43.400][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:43.401][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:43.403][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:44.677][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:44.679][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:44.680][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:44.681][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:46.029][private$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[2024-05-09 05:22:46.030][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:46.032][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:46.034][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:47.327][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:47.329][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:47.330][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:47.332][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:48.682][private$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[2024-05-09 05:22:48.683][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:48.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:48.686][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-09 05:22:49.970][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-09 05:22:49.972][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-09 05:22:49.973][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-09 05:22:49.975][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-09 05:22:51.326][private$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[2024-05-09 05:22:51.330][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-05-09 05:22:51.332][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-09 05:22:51.334][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-09 05:22:51.335][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-09 05:22:51.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:22:51.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:22:51.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:22:51.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:22:51.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:22:51.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:22:51.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:22:51.352][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:22:51.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:22:51.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.358][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:22:51.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:22:51.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:22:51.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:22:51.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:22:51.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:22:51.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:22:51.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:22:51.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:22:51.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:22:51.383][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:22:51.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:22:51.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.388][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:22:51.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:22:51.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:22:51.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:22:51.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:22:51.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:22:51.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:22:51.451][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-09 05:22:51.453][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-09 05:22:51.454][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-05-09 05:22:51.729][biodb::testThat]
biodb.INFO [2024-05-09 05:22:51.731][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-09 05:22:51.732][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:22:51.733][biodb::testThat]
biodb.INFO [2024-05-09 05:22:51.795][biodb::testThat]
biodb.INFO [2024-05-09 05:22:51.796][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-09 05:22:51.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:22:51.799][biodb::testThat]
biodb.INFO [2024-05-09 05:22:51.811][biodb::testThat]
biodb.INFO [2024-05-09 05:22:51.812][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-09 05:22:51.814][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:22:51.815][biodb::testThat]
biodb.DEBUG[2024-05-09 05:22:51.820][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[2024-05-09 05:22:51.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:22:51.826][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:22:51.828][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-05-09 05:22:56.728][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-05-09 05:23:19.417][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:23:19.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-05-09 05:23:19.452][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-05-09 05:23:20.797][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:20.799][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:20.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:20.801][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:20.803][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:20.804][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:20.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:20.807][ef$get] fields variable is a list.
biodb.INFO [2024-05-09 05:23:20.809][biodb::testThat]
biodb.INFO [2024-05-09 05:23:20.810][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-09 05:23:20.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:23:20.813][biodb::testThat]
biodb.ERROR[2024-05-09 05:23:20.831][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-09 05:23:20.855][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-09 05:23:20.874][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-09 05:23:20.875][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-09 05:23:20.877][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-09 05:23:20.878][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-09 05:23:20.879][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:20.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:20.881][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:20.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:20.884][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-09 05:23:20.898][biodb::testContext]
biodb.INFO [2024-05-09 05:23:20.900][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-09 05:23:20.901][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-05-09 05:23:20.902][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-09 05:23:20.904][biodb::testContext]
biodb.INFO [2024-05-09 05:23:20.906][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-09 05:23:20.908][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-09 05:23:20.913][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:23:20.915][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-09 05:23:20.917][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-09 05:23:20.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.922][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-09 05:23:20.923][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-09 05:23:20.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.928][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-09 05:23:20.929][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-09 05:23:20.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.934][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-09 05:23:20.936][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-09 05:23:20.937][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-09 05:23:20.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.942][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-09 05:23:20.943][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-09 05:23:20.945][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-09 05:23:20.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.949][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-09 05:23:20.951][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-09 05:23:20.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.956][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-09 05:23:20.957][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-09 05:23:20.959][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-09 05:23:20.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.964][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-09 05:23:20.965][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-09 05:23:20.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.970][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-09 05:23:20.971][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-09 05:23:20.973][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-09 05:23:20.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.977][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-09 05:23:20.979][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-09 05:23:20.980][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-09 05:23:20.982][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-09 05:23:20.983][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-09 05:23:20.984][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-09 05:23:20.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.989][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-09 05:23:20.991][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-09 05:23:20.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:20.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:20.995][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-09 05:23:20.997][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-09 05:23:20.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:20.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.002][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-09 05:23:21.003][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-09 05:23:21.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.008][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-09 05:23:21.010][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-09 05:23:21.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.014][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-09 05:23:21.016][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-09 05:23:21.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.021][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-09 05:23:21.022][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-09 05:23:21.027][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-09 05:23:21.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.031][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-09 05:23:21.033][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-09 05:23:21.034][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-09 05:23:21.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.039][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-09 05:23:21.042][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.043][self$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[2024-05-09 05:23:21.044][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.045][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:21.047][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.048][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.049][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.051][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.052][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:23:21.053][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:21.055][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.056][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-09 05:23:21.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:21.058][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.060][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.061][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:23:21.061][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:23:21.061][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-09 05:23:21.061][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-09 05:23:21.061][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-09 05:23:21.062][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:21.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.066][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:21.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.070][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.071][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.072][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:21.073][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:21.075][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.076][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.078][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-09 05:23:21.080][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.081][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-09 05:23:21.082][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.084][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:21.085][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.086][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.088][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.089][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.090][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-09 05:23:21.092][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:21.093][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.094][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-09 05:23:21.096][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:21.097][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.098][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.100][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:23:21.100][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:23:21.100][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-09 05:23:21.100][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-09 05:23:21.100][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-09 05:23:21.101][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:21.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:21.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.108][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.110][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.111][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:21.112][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:21.114][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.115][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.116][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-09 05:23:21.119][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.120][self$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[2024-05-09 05:23:21.122][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.123][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:21.124][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.127][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.128][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.130][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:23:21.131][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:21.132][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.134][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-09 05:23:21.135][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:21.136][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.137][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.139][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.140][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:21.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.144][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:21.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.149][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.150][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:21.151][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:21.152][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.154][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.155][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-09 05:23:21.157][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.159][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-09 05:23:21.160][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.162][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:21.163][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.164][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.165][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.167][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.168][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-09 05:23:21.169][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:21.171][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.172][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-09 05:23:21.173][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:21.175][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.176][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.177][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.179][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:21.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.183][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:21.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.186][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.188][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.189][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:21.190][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:21.192][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.193][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.195][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:23:21.196][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.203][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[2024-05-09 05:23:21.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.209][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[2024-05-09 05:23:21.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.253][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[2024-05-09 05:23:21.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.259][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[2024-05-09 05:23:21.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.300][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[2024-05-09 05:23:21.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.305][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[2024-05-09 05:23:21.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.330][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-09 05:23:21.332][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-09 05:23:21.334][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-09 05:23:21.336][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-09 05:23:21.338][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-09 05:23:21.340][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-09 05:23:21.342][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-09 05:23:21.343][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-09 05:23:21.345][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-09 05:23:21.347][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-09 05:23:21.349][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-09 05:23:21.351][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-09 05:23:21.353][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-09 05:23:21.355][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-09 05:23:21.356][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-09 05:23:21.358][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-09 05:23:21.360][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-09 05:23:21.362][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-09 05:23:21.364][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-09 05:23:21.366][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-09 05:23:21.368][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-09 05:23:21.370][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-09 05:23:21.372][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-09 05:23:21.373][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-09 05:23:21.375][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-09 05:23:21.377][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-09 05:23:21.379][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-09 05:23:21.381][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-09 05:23:21.383][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-09 05:23:21.385][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-09 05:23:21.387][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-09 05:23:21.389][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-09 05:23:21.391][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-09 05:23:21.393][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-09 05:23:21.394][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-09 05:23:21.396][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-09 05:23:21.398][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-09 05:23:21.400][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-09 05:23:21.402][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-09 05:23:21.404][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-09 05:23:21.406][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-09 05:23:21.408][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-09 05:23:21.410][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-09 05:23:21.412][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-09 05:23:21.413][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-09 05:23:21.415][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-09 05:23:21.417][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-09 05:23:21.419][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-09 05:23:21.421][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-09 05:23:21.423][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-09 05:23:21.425][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-09 05:23:21.427][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-09 05:23:21.429][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-09 05:23:21.431][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-09 05:23:21.433][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-09 05:23:21.434][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-09 05:23:21.436][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-09 05:23:21.438][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-09 05:23:21.440][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-09 05:23:21.442][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-09 05:23:21.444][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-09 05:23:21.446][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-09 05:23:21.448][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-09 05:23:21.450][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-09 05:23:21.452][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-09 05:23:21.454][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-09 05:23:21.456][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-09 05:23:21.458][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-09 05:23:21.459][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-09 05:23:21.461][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-09 05:23:21.463][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-09 05:23:21.465][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-09 05:23:21.467][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-09 05:23:21.469][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-09 05:23:21.471][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-09 05:23:21.473][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-09 05:23:21.475][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-09 05:23:21.477][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-09 05:23:21.479][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-09 05:23:21.481][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-09 05:23:21.483][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-09 05:23:21.484][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-09 05:23:21.486][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-09 05:23:21.488][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-09 05:23:21.490][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-09 05:23:21.492][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:23:21.493][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.495][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.530][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[2024-05-09 05:23:21.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.539][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[2024-05-09 05:23:21.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.556][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[2024-05-09 05:23:21.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.581][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[2024-05-09 05:23:21.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.597][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[2024-05-09 05:23:21.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.606][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[2024-05-09 05:23:21.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.614][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[2024-05-09 05:23:21.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.622][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[2024-05-09 05:23:21.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:21.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:21.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:21.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:21.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:21.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:21.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:21.641][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-09 05:23:21.643][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:23:21.646][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.647][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.648][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.650][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:21.651][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.652][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.654][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.655][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.656][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:23:21.658][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:21.659][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.660][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-09 05:23:21.662][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-09 05:23:21.663][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-09 05:23:21.664][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:21.666][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:23:21.666][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:23:21.667][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:21.668][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.669][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.671][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:21.672][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:21.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:21.689][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:21.691][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-09 05:23:21.691][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-09 05:23:21.693][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:21.694][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:21.695][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:21.696][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:21.698][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-09 05:23:21.700][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-09 05:23:21.704][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:23:21.706][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-09 05:23:21.707][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:23:21.709][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-09 05:23:21.711][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-09 05:23:21.712][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-09 05:23:21.714][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-09 05:23:21.715][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-09 05:23:21.717][biodb::testThat]
biodb.INFO [2024-05-09 05:23:21.718][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-05-09 05:23:21.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:23:21.721][biodb::testThat]
biodb.DEBUG[2024-05-09 05:23:21.726][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-05-09 05:23:21.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:23:21.733][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:23:21.735][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-05-09 05:23:23.045][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[2024-05-09 05:23:24.400][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:23:24.402][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-05-09 05:23:24.407][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-05-09 05:23:24.419][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[2024-05-09 05:23:24.424][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:23:24.425][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:23:24.428][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-05-09 05:23:25.760][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-05-09 05:23:27.074][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:23:27.077][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-05-09 05:23:27.082][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-05-09 05:23:27.096][biodb::testThat]
biodb.INFO [2024-05-09 05:23:27.097][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-05-09 05:23:27.099][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:23:27.100][biodb::testThat]
biodb.INFO [2024-05-09 05:23:27.136][biodb::testThat]
biodb.INFO [2024-05-09 05:23:27.137][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-05-09 05:23:27.139][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:23:27.140][biodb::testThat]
biodb.DEBUG[2024-05-09 05:23:27.144][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-09 05:23:27.149][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:23:27.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:23:27.153][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-05-09 05:23:28.272][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-05-09 05:23:29.422][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:23:29.425][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-05-09 05:23:29.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-05-09 05:23:29.438][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[2024-05-09 05:23:29.442][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-09 05:23:29.444][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-09 05:23:29.445][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-09 05:23:29.447][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-09 05:23:29.456][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[2024-05-09 05:23:29.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:23:29.462][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:23:29.465][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-05-09 05:23:30.606][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-05-09 05:23:31.740][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:23:31.743][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-05-09 05:23:31.749][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-05-09 05:23:31.759][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-05-09 05:23:31.764][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:23:31.765][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:23:31.768][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-05-09 05:23:33.718][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-05-09 05:23:42.619][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:23:42.622][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-05-09 05:23:42.630][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-05-09 05:23:42.788][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[2024-05-09 05:23:42.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-09 05:23:42.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-09 05:23:42.798][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-05-09 05:23:44.705][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-05-09 05:23:53.352][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-09 05:23:53.355][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-05-09 05:23:53.362][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-05-09 05:23:53.517][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-09 05:23:53.519][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-09 05:23:53.521][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-09 05:23:53.522][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-09 05:23:53.524][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:53.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:53.526][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.529][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-09 05:23:53.535][biodb::testContext]
biodb.INFO [2024-05-09 05:23:53.536][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-09 05:23:53.537][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-05-09 05:23:53.539][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-09 05:23:53.540][biodb::testContext]
biodb.INFO [2024-05-09 05:23:53.543][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-09 05:23:53.545][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-09 05:23:53.550][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:23:53.552][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-09 05:23:53.553][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-09 05:23:53.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.558][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-09 05:23:53.560][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-09 05:23:53.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.565][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-09 05:23:53.566][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-09 05:23:53.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.572][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-09 05:23:53.573][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-09 05:23:53.574][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-09 05:23:53.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.579][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-09 05:23:53.581][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-09 05:23:53.582][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-09 05:23:53.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.586][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[2024-05-09 05:23:53.587][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-09 05:23:53.589][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-09 05:23:53.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.594][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-09 05:23:53.595][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-09 05:23:53.597][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-09 05:23:53.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.600][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[2024-05-09 05:23:53.602][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-09 05:23:53.603][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-09 05:23:53.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.608][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-09 05:23:53.610][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-09 05:23:53.611][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-09 05:23:53.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.615][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[2024-05-09 05:23:53.616][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-09 05:23:53.618][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-09 05:23:53.619][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-09 05:23:53.620][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-09 05:23:53.622][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-09 05:23:53.623][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-09 05:23:53.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.629][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-09 05:23:53.630][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-09 05:23:53.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.634][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[2024-05-09 05:23:53.635][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-09 05:23:53.637][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-09 05:23:53.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.642][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-09 05:23:53.644][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-09 05:23:53.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.649][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-09 05:23:53.651][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-09 05:23:53.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.656][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-09 05:23:53.658][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-09 05:23:53.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.663][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-09 05:23:53.664][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-09 05:23:53.669][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-09 05:23:53.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.674][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-09 05:23:53.676][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-09 05:23:53.677][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-09 05:23:53.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.682][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-09 05:23:53.685][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.686][self$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[2024-05-09 05:23:53.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.727][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:53.729][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.730][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.731][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.733][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.734][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:23:53.735][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:53.737][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.738][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-09 05:23:53.739][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:53.741][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.742][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.743][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:23:53.743][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:23:53.743][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-09 05:23:53.743][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-09 05:23:53.743][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-09 05:23:53.745][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:53.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:53.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:53.749][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:53.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:53.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:53.754][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.755][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.757][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:53.758][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:53.759][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.761][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.762][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-09 05:23:53.765][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.767][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-09 05:23:53.768][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.770][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:53.771][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.772][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.774][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.777][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-09 05:23:53.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:53.780][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.781][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-09 05:23:53.783][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:53.784][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.786][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.787][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:23:53.787][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:23:53.787][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-09 05:23:53.787][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-09 05:23:53.787][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-09 05:23:53.788][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:53.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:53.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:53.793][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:53.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:53.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:53.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.798][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.799][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:53.801][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:53.802][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.803][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.805][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-09 05:23:53.807][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.809][self$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[2024-05-09 05:23:53.810][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.812][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:53.813][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.815][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.816][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.817][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.819][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:23:53.820][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:53.821][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.823][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-09 05:23:53.824][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:53.826][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.827][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.828][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.830][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:53.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:53.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:53.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:53.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:53.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:53.837][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.839][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:53.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:53.843][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.844][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.846][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-09 05:23:53.848][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.849][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-09 05:23:53.851][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.852][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:53.853][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.855][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.856][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.858][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.859][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-09 05:23:53.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:53.862][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.863][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-09 05:23:53.865][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:53.866][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.867][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:53.869][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.870][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:53.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:53.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:53.874][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:53.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:53.877][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:53.878][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:53.880][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.881][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:53.882][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:53.884][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:53.885][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:53.887][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:23:53.888][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.942][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[2024-05-09 05:23:53.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.961][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[2024-05-09 05:23:53.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:53.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:53.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:53.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:53.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:53.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.002][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-09 05:23:54.004][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-09 05:23:54.006][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-09 05:23:54.008][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-09 05:23:54.010][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-09 05:23:54.012][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-09 05:23:54.014][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-09 05:23:54.016][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-09 05:23:54.019][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-09 05:23:54.021][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-09 05:23:54.023][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-09 05:23:54.025][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-09 05:23:54.027][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-09 05:23:54.030][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-09 05:23:54.032][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-09 05:23:54.034][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-09 05:23:54.036][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-09 05:23:54.038][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-09 05:23:54.040][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-09 05:23:54.042][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-09 05:23:54.044][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-09 05:23:54.046][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-09 05:23:54.048][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-09 05:23:54.050][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-09 05:23:54.052][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-09 05:23:54.054][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-09 05:23:54.056][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-09 05:23:54.058][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-09 05:23:54.060][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-09 05:23:54.062][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-09 05:23:54.064][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-09 05:23:54.066][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-09 05:23:54.068][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-09 05:23:54.070][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-09 05:23:54.072][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-09 05:23:54.074][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-09 05:23:54.076][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-09 05:23:54.078][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-09 05:23:54.080][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-09 05:23:54.082][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-09 05:23:54.084][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-09 05:23:54.086][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-09 05:23:54.088][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-09 05:23:54.090][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-09 05:23:54.092][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-09 05:23:54.094][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-09 05:23:54.096][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-09 05:23:54.098][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-09 05:23:54.100][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-09 05:23:54.102][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-09 05:23:54.104][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-09 05:23:54.106][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-09 05:23:54.108][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-09 05:23:54.110][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-09 05:23:54.112][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-09 05:23:54.114][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-09 05:23:54.116][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-09 05:23:54.118][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-09 05:23:54.120][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-09 05:23:54.122][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-09 05:23:54.124][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-09 05:23:54.126][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-09 05:23:54.128][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-09 05:23:54.130][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-09 05:23:54.132][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-09 05:23:54.134][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-09 05:23:54.136][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-09 05:23:54.138][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-09 05:23:54.140][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-09 05:23:54.142][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-09 05:23:54.144][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-09 05:23:54.146][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-09 05:23:54.148][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-09 05:23:54.150][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-09 05:23:54.152][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-09 05:23:54.154][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-09 05:23:54.156][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-09 05:23:54.158][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-09 05:23:54.160][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-09 05:23:54.163][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-09 05:23:54.165][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-09 05:23:54.168][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-09 05:23:54.170][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-09 05:23:54.172][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-09 05:23:54.174][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-09 05:23:54.176][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-09 05:23:54.177][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.196][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.238][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[2024-05-09 05:23:54.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.247][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[2024-05-09 05:23:54.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.255][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[2024-05-09 05:23:54.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-09 05:23:54.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-09 05:23:54.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:54.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:54.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:54.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:54.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:54.342][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[2024-05-09 05:23:54.344][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-09 05:23:54.346][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:23:54.348][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:54.349][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-09 05:23:54.351][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:54.352][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-09 05:23:54.354][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:54.355][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-09 05:23:54.357][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:54.358][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-09 05:23:54.360][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-09 05:23:54.361][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-09 05:23:54.362][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:54.364][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-09 05:23:54.365][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-09 05:23:54.367][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-09 05:23:54.369][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-09 05:23:54.370][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-09 05:23:54.370][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-09 05:23:54.372][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-09 05:23:54.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:54.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:54.376][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-09 05:23:54.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-09 05:23:54.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-09 05:23:54.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-09 05:23:54.381][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-09 05:23:54.381][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-09 05:23:54.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-09 05:23:54.384][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-09 05:23:54.385][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-09 05:23:54.386][self$setPropertyValue]
biodb.DEBUG[2024-05-09 05:23:54.388][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-09 05:23:54.390][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-09 05:23:54.394][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:23:54.396][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-09 05:23:54.397][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-09 05:23:54.400][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-09 05:23:54.401][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-09 05:23:54.402][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-09 05:23:54.404][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-09 05:23:54.406][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-09 05:23:54.408][biodb::testThat]
biodb.INFO [2024-05-09 05:23:54.409][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-05-09 05:23:54.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-09 05:23:54.412][biodb::testThat]
biodb.DEBUG[2024-05-09 05:23:54.417][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-09 05:23:54.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-09 05:23:54.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-09 05:23:54.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-09 05:23:54.522][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-05-09 05:23:55.645][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-05-09 05:23:55.647][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-09 05:23:55.649][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-05-09 05:23:55.651][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-09 05:23:55.653][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-05-09 05:23:55.654][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-09 05:23:55.656][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-09 05:23:55.658][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-09 05:23:55.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:23:55.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:55.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:55.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:55.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:55.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:55.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:23:55.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:55.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:55.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:55.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:55.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:55.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:55.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:55.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:55.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.705][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:23:55.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:23:55.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:23:55.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:23:55.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.717][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:55.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:55.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.723][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:55.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:55.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.729][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:55.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:55.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.735][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:55.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:55.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.741][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:23:55.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:55.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.747][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:23:55.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:55.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:55.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:55.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:55.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:55.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:23:55.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.783][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-09 05:23:55.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.801][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:23:55.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.837][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:55.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:55.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.843][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:55.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:55.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:55.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.855][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:55.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:55.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:55.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:55.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:55.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:55.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:55.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:55.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:23:55.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:23:55.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:55.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:55.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:55.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:55.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:55.891][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.TRACE[2024-05-09 05:23:55.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:55.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:55.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:55.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:55.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:55.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:55.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:55.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:55.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.921][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:23:55.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-09 05:23:55.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.927][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:23:55.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-09 05:23:55.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.933][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:55.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:55.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.939][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:55.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:55.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.945][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:55.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.951][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:55.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:55.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.957][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:23:55.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:55.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.963][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-09 05:23:55.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:55.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.969][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:55.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:55.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:55.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:55.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:55.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.992][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:23:55.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:55.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:55.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:55.998][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-09 05:23:56.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.015][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-09 05:23:56.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.021][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.038][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-09 05:23:56.096][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-05-09 05:23:56.099][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-09 05:23:56.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:23:56.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:56.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:56.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:56.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:56.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:56.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:23:56.145][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:23:56.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:23:56.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:23:56.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:23:56.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.156][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-09 05:23:56.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-09 05:23:56.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-09 05:23:56.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-09 05:23:56.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.167][private$selectFields] Fields none
biodb.TRACE[2024-05-09 05:23:56.168][private$selectFields]
biodb.TRACE[2024-05-09 05:23:56.170][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-09 05:23:56.171][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:23:56.172][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:23:56.174][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.175][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.178][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.179][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.181][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.184][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.185][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.187][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.189][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.191][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.192][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.196][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.197][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.201][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.203][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.204][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.207][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.208][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.210][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.212][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.214][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.215][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.218][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.219][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.221][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.223][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.229][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.230][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.231][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.234][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.235][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.237][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.240][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.241][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.242][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.245][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.246][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.248][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.250][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.252][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.253][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.256][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.257][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.259][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.261][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.263][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:23:56.264][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:23:56.265][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.267][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.269][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.275][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.276][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.278][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.280][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.282][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.283][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.286][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.287][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.288][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.291][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.292][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.294][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.296][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.298][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.302][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.303][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.305][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.308][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.309][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-05-09 05:23:56.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.345][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.350][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.355][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.367][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.395][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.401][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.406][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.429][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.435][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.440][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.454][private$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[2024-05-09 05:23:56.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-09 05:23:56.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:56.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:56.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:56.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:56.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:56.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-09 05:23:56.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:23:56.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:23:56.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-09 05:23:56.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-09 05:23:56.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-09 05:23:56.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-09 05:23:56.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-09 05:23:56.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-09 05:23:56.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.492][private$selectFields] Fields none
biodb.TRACE[2024-05-09 05:23:56.494][private$selectFields]
biodb.TRACE[2024-05-09 05:23:56.495][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-09 05:23:56.496][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-09 05:23:56.497][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:23:56.499][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.500][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.503][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.506][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.508][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.510][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.511][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.514][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.515][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.516][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.519][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.520][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.522][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.524][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.526][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.527][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.530][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.531][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.533][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.535][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.537][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.538][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.541][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.542][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.544][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.546][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.547][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.549][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.552][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.553][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.555][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.558][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.559][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.560][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.585][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.587][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.588][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.591][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.592][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.594][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.596][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.597][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.599][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.602][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.603][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.604][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.607][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.608][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:23:56.610][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-09 05:23:56.611][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.612][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.615][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.616][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.620][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.621][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.623][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.625][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.627][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.628][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.631][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.632][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.633][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.636][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.637][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.639][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.641][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.642][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.644][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.646][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.647][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.649][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.651][ef$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.653][private$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[2024-05-09 05:23:56.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-09 05:23:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-09 05:23:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-09 05:23:56.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.687][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.699][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-09 05:23:56.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-09 05:23:56.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-09 05:23:56.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.751][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-09 05:23:56.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-09 05:23:56.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-09 05:23:56.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-09 05:23:56.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.773][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.778][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.784][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-09 05:23:56.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-09 05:23:56.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-09 05:23:56.795][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-05-09 05:23:56.797][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-05-09 05:23:56.798][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-05-09 05:23:56.806][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-09 05:23:56.808][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-09 05:23:56.809][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-09 05:23:56.810][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-09 05:23:56.811][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-09 05:23:56.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-09 05:23:56.814][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-09 05:23:56.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-09 05:23:56.816][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-09 05:23:56.818][FUN] Functions in observer 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 166 ]

══ 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 166 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn1.0840.0565.345
LipidmapsStructureEntry0.2310.0020.234