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This page was generated on 2024-03-04 11:38:55 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 202/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: devel
git_last_commit: d096baa
git_last_commit_date: 2023-10-24 11:38:15 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for biodbLipidmaps on merida1


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

raw results


Summary

Package: biodbLipidmaps
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.9.0.tar.gz
StartedAt: 2024-03-02 00:49:10 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 00:54:46 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 335.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 4.527  1.958  24.688
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log’
for details.


Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-03-02 00:51:57.572][biodb::testContext]
biodb.INFO [2024-03-02 00:51:57.656][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:51:57.658][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-02 00:51:57.663][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:51:57.667][biodb::testContext]
biodb.INFO [2024-03-02 00:51:57.704][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:51:57.709][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 00:51:57.762][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:51:57.767][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 00:51:57.794][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 00:51:57.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:57.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:57.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:57.830][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 00:51:57.941][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 00:51:57.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:57.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:57.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:57.967][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 00:51:57.983][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 00:51:57.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:57.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:57.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.009][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 00:51:58.012][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 00:51:58.015][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 00:51:58.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.040][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 00:51:58.053][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 00:51:58.056][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 00:51:58.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.079][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 00:51:58.082][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 00:51:58.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.105][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 00:51:58.107][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 00:51:58.122][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 00:51:58.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.144][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 00:51:58.147][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 00:51:58.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.173][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 00:51:58.175][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 00:51:58.190][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 00:51:58.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.241][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:51:58.256][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 00:51:58.258][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 00:51:58.260][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 00:51:58.262][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 00:51:58.265][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 00:51:58.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.285][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 00:51:58.287][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 00:51:58.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.306][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 00:51:58.319][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 00:51:58.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.326][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 00:51:58.341][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 00:51:58.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.351][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 00:51:58.364][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 00:51:58.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.373][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 00:51:58.394][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 00:51:58.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.403][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:51:58.414][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 00:51:58.665][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 00:51:58.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.672][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 00:51:58.674][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 00:51:58.677][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 00:51:58.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:58.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:58.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:58.688][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 00:51:58.824][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:58.879][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 00:51:58.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:58.887][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:51:58.889][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:58.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:51:58.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:58.896][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:51:58.898][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:51:58.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:51:58.901][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:58.903][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 00:51:58.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:51:58.908][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:58.910][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:58.913][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:51:58.913][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:51:58.913][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:51:58.913][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:51:58.913][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:51:58.924][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:51:58.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:51:58.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:51:58.930][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:51:58.932][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:51:58.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:51:58.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:51:58.938][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:58.940][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:51:58.942][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:51:58.944][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:58.946][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:58.949][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 00:51:58.953][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:58.957][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:51:58.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:58.961][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:51:58.963][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:58.967][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:51:58.969][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:58.972][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:51:58.974][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:51:58.981][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:51:58.984][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:58.986][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 00:51:58.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:51:58.990][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:58.993][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:58.996][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:51:58.996][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:51:58.996][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:51:58.996][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:51:58.996][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:51:58.998][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:51:59.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:51:59.006][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:51:59.009][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:51:59.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:51:59.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:51:59.016][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:51:59.019][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:51:59.032][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:51:59.035][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:59.044][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.046][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 00:51:59.051][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:59.053][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 00:51:59.063][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:59.065][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:51:59.067][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:59.069][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:51:59.071][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:59.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:51:59.076][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:51:59.078][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:51:59.080][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:59.106][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 00:51:59.108][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:51:59.110][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.118][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:59.149][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.152][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:51:59.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:51:59.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:51:59.166][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:51:59.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:51:59.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:51:59.173][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:51:59.188][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:51:59.194][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:51:59.196][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:59.212][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.215][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 00:51:59.219][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:59.221][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:51:59.234][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:59.237][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:51:59.240][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:59.242][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:51:59.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:59.264][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:51:59.268][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:51:59.282][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:51:59.286][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:59.289][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 00:51:59.291][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:51:59.309][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.312][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:51:59.314][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:51:59.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:51:59.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:51:59.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:51:59.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:51:59.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:51:59.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:51:59.373][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.375][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:51:59.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:51:59.381][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:51:59.383][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:51:59.402][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:51:59.405][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.556][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[2024-03-02 00:51:59.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:51:59.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:51:59.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:51:59.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:51:59.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:51:59.805][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 00:51:59.828][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 00:51:59.831][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 00:51:59.845][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 00:51:59.848][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:51:59.855][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 00:51:59.858][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 00:51:59.862][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 00:51:59.870][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 00:51:59.873][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 00:51:59.876][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:51:59.894][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 00:51:59.898][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 00:51:59.902][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 00:51:59.911][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 00:51:59.916][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:51:59.919][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 00:51:59.943][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 00:51:59.946][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:51:59.950][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 00:51:59.958][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 00:51:59.962][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 00:51:59.974][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 00:51:59.978][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 00:51:59.981][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 00:51:59.998][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 00:52:00.002][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 00:52:00.005][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 00:52:00.029][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 00:52:00.033][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 00:52:00.036][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 00:52:00.048][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 00:52:00.052][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 00:52:00.055][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 00:52:00.060][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 00:52:00.063][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 00:52:00.083][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 00:52:00.087][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 00:52:00.090][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 00:52:00.099][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 00:52:00.103][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 00:52:00.106][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 00:52:00.127][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 00:52:00.130][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 00:52:00.133][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 00:52:00.137][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 00:52:00.153][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 00:52:00.155][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 00:52:00.159][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 00:52:00.162][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 00:52:00.178][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 00:52:00.181][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 00:52:00.184][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 00:52:00.188][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 00:52:00.191][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 00:52:00.195][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 00:52:00.198][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 00:52:00.206][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 00:52:00.210][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 00:52:00.222][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 00:52:00.226][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 00:52:00.230][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 00:52:00.243][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 00:52:00.246][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 00:52:00.250][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 00:52:00.260][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 00:52:00.264][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:52:00.268][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:52:00.282][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 00:52:00.285][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 00:52:00.288][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 00:52:00.311][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 00:52:00.314][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 00:52:00.317][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 00:52:00.339][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 00:52:00.343][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 00:52:00.347][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 00:52:00.366][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 00:52:00.369][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 00:52:00.373][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 00:52:00.391][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 00:52:00.394][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 00:52:00.397][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 00:52:00.458][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 00:52:00.466][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:52:00.477][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:52:00.479][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.496][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.731][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[2024-03-02 00:52:00.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:00.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.933][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[2024-03-02 00:52:00.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:00.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:00.966][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[2024-03-02 00:52:00.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:00.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:00.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:00.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:00.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:01.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:01.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:01.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:01.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:01.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:01.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:01.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:01.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:01.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:01.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:01.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:01.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:01.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:01.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:01.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:01.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:01.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:01.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:01.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:01.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:01.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:01.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:01.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:01.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:52:01.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:01.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:01.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:01.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:01.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:01.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:01.177][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-02 00:52:01.226][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:52:01.237][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:52:01.240][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-02 00:52:01.242][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:52:01.245][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:52:01.254][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:52:01.258][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:52:01.261][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 00:52:01.263][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:52:01.276][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:52:01.279][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:52:01.282][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:52:01.298][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-02 00:52:01.300][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-02 00:52:01.303][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-02 00:52:01.306][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 00:52:01.319][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:52:01.319][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:52:01.322][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:52:01.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:52:01.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:52:01.341][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:52:01.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:52:01.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:52:01.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:52:01.361][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-02 00:52:01.361][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-02 00:52:01.363][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:52:01.365][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:52:01.367][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 00:52:01.379][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:52:01.404][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-02 00:52:01.420][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:52:01.533][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:52:01.551][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-02 00:52:01.624][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:52:01.630][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-02 00:52:01.653][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-02 00:52:01.655][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-02 00:52:01.658][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-02 00:52:01.660][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-02 00:52:01.705][biodb::testThat]
biodb.INFO [2024-03-02 00:52:01.707][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-03-02 00:52:01.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:01.721][biodb::testThat]
biodb.TRACE[2024-03-02 00:52:01.730][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-03-02 00:52:01.748][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:52:01.754][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-02 00:52:01.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:01.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:01.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:01.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:01.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:01.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:01.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:52:01.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:01.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:01.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:01.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:01.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:01.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:01.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:01.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:01.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:52:01.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:52:01.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:01.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:01.955][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:52:01.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:52:01.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:01.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:01.961][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:52:01.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:52:01.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:01.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:01.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:01.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:01.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:01.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.047][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:02.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:02.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:02.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:02.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.064][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:02.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:02.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.069][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:52:02.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:02.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.078][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:52:02.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:02.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.083][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:02.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:02.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:02.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:02.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:52:02.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.134][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-02 00:52:02.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.169][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:52:02.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.217][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:02.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:02.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.351][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.364][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.381][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:02.458][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-02 00:52:02.464][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:52:02.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:52:02.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.476][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:52:02.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:52:02.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 00:52:02.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 00:52:02.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 00:52:02.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 00:52:02.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.723][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.892][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.903][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.913][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:02.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:02.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:02.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:02.995][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:02.997][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:03.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.006][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:03.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:03.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:03.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:03.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:03.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:03.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:03.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:03.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.093][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:03.104][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:03.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.109][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:03.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:03.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.224][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.249][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.251][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.274][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.276][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:03.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:03.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:03.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:03.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.394][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:03.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:03.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.417][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:03.419][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:03.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.437][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.439][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:03.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:03.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.576][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.579][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.583][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.667][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.695][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.726][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.744][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.751][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.767][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:03.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.840][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:03.854][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:03.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.861][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.887][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.890][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:03.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.905][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.939][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:03.942][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:03.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:03.960][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:03.985][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.988][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:03.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.007][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.031][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:04.034][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.038][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.059][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:04.068][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:04.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.073][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 00:52:04.108][biodb::testThat]
biodb.INFO [2024-03-02 00:52:04.110][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-02 00:52:04.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:04.123][biodb::testThat]
biodb.DEBUG[2024-03-02 00:52:04.167][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-03-02 00:52:04.268][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:52:04.274][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-03-02 00:52:04.278][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:52:04.281][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-03-02 00:52:04.284][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:52:04.398][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:52:04.401][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-02 00:52:04.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:04.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:04.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:04.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:04.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:04.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:04.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:52:04.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:04.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:04.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:04.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:04.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:52:04.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:52:04.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:52:04.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:52:04.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.494][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:52:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:52:04.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.510][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:52:04.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:52:04.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.519][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:04.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:04.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:04.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:04.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.644][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:04.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:04.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.668][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:04.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:04.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.701][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:52:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:04.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.722][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:52:04.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:04.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.743][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:04.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:04.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:04.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:04.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:04.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.827][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:04.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.875][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:52:04.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.895][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-02 00:52:04.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:04.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.934][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:04.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.955][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:52:04.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:04.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:04.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:04.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:04.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:04.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:05.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:05.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:05.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:05.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:05.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:05.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.083][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:05.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:05.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.107][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:05.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:05.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:05.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:05.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.164][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:05.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:05.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:05.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:05.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:05.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:05.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:05.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:05.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:05.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:05.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:05.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:05.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:05.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:05.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:05.329][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-02 00:52:05.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-02 00:52:05.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-02 00:52:05.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-02 00:52:05.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-02 00:52:05.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-02 00:52:05.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-02 00:52:05.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:52:05.434][biodb::testThat]
biodb.INFO [2024-03-02 00:52:05.436][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-02 00:52:05.454][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:05.456][biodb::testThat]
biodb.TRACE[2024-03-02 00:52:05.462][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:05.477][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:05.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.482][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:05.493][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-03-02 00:52:05.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:05.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:05.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:05.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:05.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:05.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:05.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:05.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:05.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:05.726][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-02 00:52:05.775][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-02 00:52:05.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:52:05.920][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:52:05.924][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-03-02 00:52:07.268][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-03-02 00:52:07.895][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:52:07.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-03-02 00:52:07.965][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-03-02 00:52:07.971][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-03-02 00:52:08.015][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:08.026][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:08.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:08.031][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 00:52:08.049][biodb::testThat]
biodb.INFO [2024-03-02 00:52:08.053][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-03-02 00:52:08.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:08.058][biodb::testThat]
biodb.TRACE[2024-03-02 00:52:08.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:08.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:08.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:08.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:08.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:08.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:08.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:08.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:08.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:08.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:08.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:08.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:08.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-02 00:52:08.666][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:52:08.706][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-02 00:52:08.709][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:52:08.719][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-03-02 00:52:08.802][biodb::testThat]
biodb.INFO [2024-03-02 00:52:08.804][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-03-02 00:52:08.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:08.808][biodb::testThat]
biodb.TRACE[2024-03-02 00:52:08.896][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:52:08.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:52:08.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:08.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:08.911][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:52:08.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:52:08.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:08.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:08.921][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 00:52:08.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 00:52:08.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:08.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:08.934][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 00:52:08.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 00:52:08.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:08.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:09.093][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:52:09.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:52:09.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:09.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:09.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:52:09.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:52:09.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:09.134][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 00:52:09.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 00:52:09.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:09.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:09.148][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 00:52:09.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 00:52:09.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:09.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:52:09.195][biodb::testThat]
biodb.INFO [2024-03-02 00:52:09.197][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-02 00:52:09.199][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:09.201][biodb::testThat]
biodb.INFO [2024-03-02 00:52:09.232][biodb::testThat]
biodb.INFO [2024-03-02 00:52:09.233][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-02 00:52:09.235][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:09.236][biodb::testThat]
biodb.INFO [2024-03-02 00:52:09.256][biodb::testThat]
biodb.INFO [2024-03-02 00:52:09.266][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-02 00:52:09.267][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:09.269][biodb::testThat]
biodb.DEBUG[2024-03-02 00:52:09.287][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-03-02 00:52:10.082][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-03-02 00:52:10.489][biodb::testThat]
biodb.INFO [2024-03-02 00:52:10.491][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-02 00:52:10.493][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:10.495][biodb::testThat]
biodb.TRACE[2024-03-02 00:52:10.507][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:10.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:10.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:10.515][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:10.517][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:10.526][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:10.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:10.530][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 00:52:10.534][biodb::testThat]
biodb.INFO [2024-03-02 00:52:10.536][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-03-02 00:52:10.539][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:10.541][biodb::testThat]
biodb.TRACE[2024-03-02 00:52:10.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:10.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:10.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:10.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:10.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:10.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:10.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:10.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:10.629][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:10.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:10.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:10.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:10.983][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-02 00:52:10.990][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:52:10.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-02 00:52:10.997][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:52:11.001][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-03-02 00:52:11.238][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-02 00:52:11.252][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:52:11.256][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-02 00:52:11.259][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:52:11.266][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-03-02 00:52:11.312][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-02 00:52:11.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-02 00:52:11.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:11.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:11.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:52:11.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:52:11.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:11.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:11.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:11.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:11.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:11.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:11.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:11.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:11.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:11.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:11.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:11.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:11.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:11.457][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-03-02 00:52:11.505][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:52:11.507][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:52:11.566][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-03-02 00:52:15.542][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-03-02 00:52:24.233][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:52:24.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-03-02 00:52:24.911][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-03-02 00:52:29.568][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-03-02 00:52:29.577][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:52:29.580][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:52:29.602][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-03-02 00:52:30.259][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-03-02 00:52:30.925][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:52:30.940][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-03-02 00:52:30.949][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-03-02 00:52:31.000][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-03-02 00:52:31.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:52:31.006][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:52:31.009][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-03-02 00:52:31.680][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-03-02 00:52:32.320][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:52:32.325][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-03-02 00:52:32.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-03-02 00:52:32.372][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-02 00:52:32.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-02 00:52:32.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:32.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:52:32.395][biodb::testThat]
biodb.INFO [2024-03-02 00:52:32.397][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-02 00:52:32.400][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:32.402][biodb::testThat]
biodb.TRACE[2024-03-02 00:52:32.408][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-02 00:52:32.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-02 00:52:32.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:32.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:32.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:52:32.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:52:32.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:32.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:32.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:32.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:32.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:32.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:32.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:32.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:32.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:32.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:32.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:32.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:32.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:32.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:32.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:32.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:32.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:32.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:32.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:32.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:32.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:32.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:32.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:32.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:32.536][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-03-02 00:52:32.544][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:52:32.547][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:52:32.552][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-03-02 00:52:36.604][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-03-02 00:52:44.300][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:52:44.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-03-02 00:52:44.544][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-03-02 00:52:49.130][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-03-02 00:52:49.388][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-02 00:52:49.401][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-03-02 00:52:49.405][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-02 00:52:49.408][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:52:49.412][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:52:49.424][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-02 00:52:49.428][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:52:49.430][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:52:49.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:49.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:49.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:49.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:49.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:49.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:49.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:49.597][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-03-02 00:52:49.618][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:52:49.621][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:52:49.626][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-02 00:52:50.321][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-03-02 00:52:50.961][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:52:50.964][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-03-02 00:52:50.991][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-03-02 00:52:50.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:50.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:50.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:51.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:51.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:51.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:51.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:51.013][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-03-02 00:52:51.019][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:52:51.020][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:52:51.022][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-03-02 00:52:51.758][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-03-02 00:52:52.385][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:52:52.388][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-03-02 00:52:52.393][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-03-02 00:52:52.396][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-03-02 00:52:52.399][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:52:52.400][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-02 00:52:52.403][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-02 00:52:52.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:52.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:52.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:52.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:52.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:52.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:52.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:52:52.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:52.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:52.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:52.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:52.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:52.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:52.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:52.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:52:52.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:52:52.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:52.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:52.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:52:52.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:52:52.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:52.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:52.629][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:52:52.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:52:52.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:52.765][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:52:52.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:52:52.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:52.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:52.975][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:52.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:53.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.093][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:53.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:53.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:53.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:53.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.292][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:53.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:53.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.384][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:52:53.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:53.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.541][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:52:53.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.638][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:53.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:53.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:53.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:53.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:53.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:53.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:53.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:53.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:53.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.023][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:52:54.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:54.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.078][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-02 00:52:54.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:54.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:54.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:54.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:54.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:54.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.239][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:52:54.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:54.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.264][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:54.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:54.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.282][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:54.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:54.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:54.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.415][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:54.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:54.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:54.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:54.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:54.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:54.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:54.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:54.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:54.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:54.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:54.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:54.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:54.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:54.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:54.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:52:54.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:54.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:54.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:54.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:54.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:52:54.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:52:54.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.936][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:52:54.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:52:54.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.955][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:52:54.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:52:54.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.960][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:54.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:54.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:54.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:52:54.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.973][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:54.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:54.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.979][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:54.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:52:54.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.984][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:52:54.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:54.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:54.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:54.994][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:52:54.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:54.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.003][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:55.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:55.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:52:55.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:52:55.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:55.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:55.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:55.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:55.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.047][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:52:55.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:55.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.059][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-02 00:52:55.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:55.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:55.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:55.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:52:55.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:55.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.091][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:52:55.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:52:55.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.106][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.149][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:52:55.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:52:55.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:55.302][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-03-02 00:52:55.340][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:52:55.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:55.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:55.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:55.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:55.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:55.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:55.380][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[2024-03-02 00:52:55.382][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.398][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.424][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.426][private$selectFields]
biodb.TRACE[2024-03-02 00:52:55.429][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:52:55.435][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:52:55.438][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.441][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.443][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.446][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.448][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.452][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.459][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.461][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.462][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.464][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.465][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.469][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.471][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:52:55.474][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.487][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.499][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.545][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-02 00:52:55.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:55.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:55.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:55.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:55.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:55.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:55.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:52:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.676][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.753][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.755][private$selectFields]
biodb.TRACE[2024-03-02 00:52:55.758][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:52:55.760][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:52:55.762][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.764][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.767][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.771][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.773][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.775][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.780][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.782][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.784][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.787][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.789][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.794][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.796][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:52:55.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.848][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.859][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-02 00:52:55.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:55.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:55.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:55.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:55.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:55.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:55.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:52:55.911][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.935][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.960][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.962][private$selectFields]
biodb.TRACE[2024-03-02 00:52:55.965][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:52:55.971][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:52:55.973][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:55.975][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.977][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:55.988][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:55.990][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:55.994][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.008][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.010][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:56.018][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:52:56.021][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.026][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.036][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.052][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:52:56.056][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.159][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:52:56.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.169][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-02 00:52:56.171][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:52:56.173][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:52:56.263][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-02 00:52:56.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-02 00:52:56.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:52:56.284][biodb::testThat]
biodb.INFO [2024-03-02 00:52:56.290][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-02 00:52:56.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:52:56.295][biodb::testThat]
biodb.TRACE[2024-03-02 00:52:56.354][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-02 00:52:56.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-02 00:52:56.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:52:56.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:52:56.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:56.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:56.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:56.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:56.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:56.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:56.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:52:56.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:56.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:52:56.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:52:56.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:52:56.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:52:56.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:52:56.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:52:56.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:52:56.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:52:56.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:52:56.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:52:56.797][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-03-02 00:52:56.825][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:52:56.829][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:52:56.834][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-03-02 00:53:00.850][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-03-02 00:53:08.793][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:53:08.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-03-02 00:53:09.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-03-02 00:53:13.833][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:53:13.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:13.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:13.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:13.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:13.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:13.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:13.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:53:14.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.082][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.214][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.217][private$selectFields]
biodb.TRACE[2024-03-02 00:53:14.219][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:53:14.221][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:53:14.224][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.244][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.246][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.250][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.252][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.259][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.263][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.266][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.322][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.324][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.336][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.341][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.343][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:53:14.356][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.365][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.381][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.412][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-02 00:53:14.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:14.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:14.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:14.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:14.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:14.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:14.467][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.TRACE[2024-03-02 00:53:14.470][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.485][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.506][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.508][private$selectFields]
biodb.TRACE[2024-03-02 00:53:14.510][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:53:14.512][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:53:14.524][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.526][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.528][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.544][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.546][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.550][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.565][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.568][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.570][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.573][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.584][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.589][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.591][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:53:14.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.643][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.666][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-02 00:53:14.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:14.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:14.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:14.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:14.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:14.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:14.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:53:14.725][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.744][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.761][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.764][private$selectFields]
biodb.TRACE[2024-03-02 00:53:14.766][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:53:14.778][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:53:14.781][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.784][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.786][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.800][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.802][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.804][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.809][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.811][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.825][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:14.830][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.835][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.848][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.851][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:53:14.854][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.874][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.903][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:14.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:14.914][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-02 00:53:14.917][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:53:14.919][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:53:14.964][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-02 00:53:14.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-02 00:53:14.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:14.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:53:15.005][biodb::testThat]
biodb.INFO [2024-03-02 00:53:15.008][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-02 00:53:15.022][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:53:15.024][biodb::testThat]
biodb.TRACE[2024-03-02 00:53:15.046][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-02 00:53:15.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-02 00:53:15.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:15.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:15.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:53:15.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:53:15.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:15.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:53:15.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:53:15.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:15.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:15.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:53:15.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:53:15.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:15.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:15.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:53:15.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:53:15.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:15.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:53:15.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:53:15.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:15.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:53:15.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:15.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:15.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:15.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:15.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:15.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:15.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:53:15.247][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-03-02 00:53:15.264][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:53:15.266][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-03-02 00:53:15.276][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:53:15.369][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-03-02 00:53:17.850][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:53:17.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:17.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:17.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:17.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:17.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:17.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:17.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:53:17.884][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:17.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:17.895][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:17.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:17.905][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:17.907][private$selectFields]
biodb.TRACE[2024-03-02 00:53:17.909][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:53:17.912][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:53:17.914][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:17.917][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.919][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:17.924][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:17.927][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.929][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:17.934][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:17.936][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:17.938][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:17.941][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.944][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:17.950][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:17.953][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:53:17.955][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:17.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:17.964][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:17.974][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:17.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:17.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:17.984][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-02 00:53:17.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:17.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:17.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:18.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:18.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:18.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:18.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:53:18.011][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.021][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.030][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:18.033][private$selectFields]
biodb.TRACE[2024-03-02 00:53:18.035][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:53:18.037][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:53:18.040][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:18.042][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.044][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.049][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.052][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.054][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.058][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.061][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:18.063][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:18.065][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.068][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.073][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.076][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:53:18.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.092][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.113][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-02 00:53:18.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:18.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:18.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:18.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:18.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:18.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:18.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:53:18.140][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.150][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.160][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:18.162][private$selectFields]
biodb.TRACE[2024-03-02 00:53:18.165][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:53:18.170][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:53:18.172][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:18.175][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.178][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.183][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.185][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.188][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.193][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.196][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:18.198][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:53:18.200][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.204][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.209][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.211][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-02 00:53:18.214][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.223][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.239][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:18.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:18.255][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-02 00:53:18.257][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:53:18.259][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:53:18.314][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-02 00:53:18.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-02 00:53:18.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:18.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:53:18.334][biodb::testThat]
biodb.INFO [2024-03-02 00:53:18.340][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-03-02 00:53:18.342][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:53:18.344][biodb::testThat]
biodb.DEBUG[2024-03-02 00:53:18.348][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-02 00:53:18.351][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:53:18.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-02 00:53:18.357][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:53:18.361][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:53:18.364][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:53:18.366][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-02 00:53:18.368][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:53:18.371][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:53:18.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:18.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:18.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:18.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:18.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:18.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:18.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:53:18.442][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-03-02 00:53:18.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:18.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:18.454][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:19.048][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:19.050][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:19.053][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:19.055][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:20.118][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:20.121][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:20.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:20.126][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:20.737][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:20.739][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:20.741][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:20.744][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:21.732][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:21.734][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:21.737][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:21.740][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:22.336][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:22.338][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:22.340][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:22.342][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:23.035][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:23.038][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:23.040][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:23.042][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:23.623][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:23.625][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:23.627][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:23.629][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:24.492][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:24.494][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:24.496][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:24.499][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:25.085][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:25.087][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:25.089][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:25.091][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:25.942][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:25.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:25.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:25.949][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:26.553][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:26.555][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:26.557][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:26.559][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:27.167][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:27.169][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:27.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:27.174][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:27.778][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:27.780][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:27.782][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:27.785][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:28.349][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:28.351][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:28.353][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:28.357][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:28.884][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:28.891][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:28.957][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:28.959][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:29.741][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:29.744][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:29.746][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:29.749][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:30.309][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:30.311][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:30.314][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:30.317][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:30.866][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:30.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:30.870][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:30.873][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-02 00:53:31.427][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:31.429][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:31.431][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:31.434][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-02 00:53:32.487][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-02 00:53:32.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-03-02 00:53:32.500][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:53:32.503][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:53:32.505][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-02 00:53:32.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:32.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:32.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:32.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:32.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:32.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:32.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:53:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:32.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:32.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:32.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:32.545][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:32.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:32.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:32.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:32.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:32.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:32.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:32.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:32.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:32.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:32.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:32.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:32.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:32.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:32.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:32.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:32.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:32.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:32.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:32.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:32.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:32.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:32.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:32.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:32.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:32.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:32.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:32.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:53:32.612][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-03-02 00:53:32.614][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-02 00:53:32.633][biodb::testThat]
biodb.INFO [2024-03-02 00:53:32.635][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-02 00:53:32.637][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:53:32.639][biodb::testThat]
biodb.DEBUG[2024-03-02 00:53:32.657][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-03-02 00:53:32.660][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-03-02 00:53:32.663][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-02 00:53:32.666][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-03-02 00:53:32.669][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-02 00:53:32.672][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:53:32.674][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:53:32.676][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-02 00:53:32.679][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:53:32.681][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:53:32.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:32.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:32.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:32.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:32.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:32.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:32.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:53:32.713][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-03-02 00:53:32.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:32.721][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:32.725][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:33.269][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:33.271][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:33.273][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:33.275][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:34.260][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:34.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:34.265][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:34.268][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:34.812][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:34.814][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:34.817][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:34.820][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:35.723][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:35.726][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:35.728][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:35.731][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:36.297][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:36.299][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:36.301][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:36.304][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:37.187][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:37.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:37.191][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:37.194][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:37.763][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:37.765][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:37.767][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:37.770][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:38.327][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:38.329][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:38.332][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:38.334][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:38.892][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:38.894][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:38.896][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:38.898][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:39.691][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:39.693][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:39.695][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:39.698][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:40.237][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:40.238][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:40.239][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[2024-03-02 00:53:40.241][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:41.029][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:41.032][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:41.033][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:41.036][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:41.569][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:41.571][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:41.572][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:41.573][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:42.108][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:42.109][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:42.110][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:42.112][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:42.669][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:42.696][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:42.707][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:42.709][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:43.239][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:43.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:43.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:43.244][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:43.785][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:43.786][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:43.788][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:43.789][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:44.323][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:44.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:44.325][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:44.327][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-02 00:53:44.860][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:44.861][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:44.862][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:44.863][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-02 00:53:45.402][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:45.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:45.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:45.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:45.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:45.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:45.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:45.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:53:45.418][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-03-02 00:53:45.421][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:45.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:45.424][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:45.953][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:45.954][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:45.955][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:45.956][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:46.899][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:46.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:46.902][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:46.903][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:47.436][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:47.437][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:47.439][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:47.443][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:47.978][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:47.980][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:47.981][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:47.984][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:48.516][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:48.518][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:48.520][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:48.521][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:49.071][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:49.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:49.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:49.075][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:49.607][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:49.610][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:49.611][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:49.612][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:50.188][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:50.190][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:50.195][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:50.197][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:50.742][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:50.745][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:50.746][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:50.747][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:51.306][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:51.308][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:51.309][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:51.310][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:51.861][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:51.862][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:51.864][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:51.867][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:52.402][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:52.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:52.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:52.413][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:52.945][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:52.946][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:52.948][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:52.949][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:53.504][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:53.511][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:53.513][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:53.515][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:54.098][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:54.100][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:54.102][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:54.103][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:54.693][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:54.694][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:54.696][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:54.761][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:55.340][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:55.342][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:55.345][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:55.347][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:56.141][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-02 00:53:56.143][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:56.145][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:56.148][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-02 00:53:56.669][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-02 00:53:56.671][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-02 00:53:56.674][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-02 00:53:56.677][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-02 00:53:57.242][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-02 00:53:57.248][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-03-02 00:53:57.253][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:53:57.256][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-02 00:53:57.258][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-02 00:53:57.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:57.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:57.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:57.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:57.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:57.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:57.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:53:57.290][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:57.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:57.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.301][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:57.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:57.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:53:57.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:53:57.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:53:57.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:53:57.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:53:57.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:53:57.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:53:57.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:53:57.350][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:57.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:57.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.361][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:57.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:53:57.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:53:57.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:53:57.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:53:57.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:53:57.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:53:57.478][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-03-02 00:53:57.481][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-02 00:53:57.483][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-03-02 00:53:57.861][biodb::testThat]
biodb.INFO [2024-03-02 00:53:57.864][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-03-02 00:53:57.866][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:53:57.868][biodb::testThat]
biodb.INFO [2024-03-02 00:53:57.984][biodb::testThat]
biodb.INFO [2024-03-02 00:53:57.988][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-03-02 00:53:57.990][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:53:57.992][biodb::testThat]
biodb.INFO [2024-03-02 00:53:58.017][biodb::testThat]
biodb.INFO [2024-03-02 00:53:58.019][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-03-02 00:53:58.023][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:53:58.025][biodb::testThat]
biodb.DEBUG[2024-03-02 00:53:58.033][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-02 00:53:58.042][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:53:58.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:53:58.090][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-03-02 00:54:02.205][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-03-02 00:54:09.045][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:54:09.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-03-02 00:54:09.264][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-03-02 00:54:11.837][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:11.841][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:11.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:11.845][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:11.848][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:11.851][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:11.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:11.855][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 00:54:11.859][biodb::testThat]
biodb.INFO [2024-03-02 00:54:11.862][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-02 00:54:11.864][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:54:11.866][biodb::testThat]
biodb.ERROR[2024-03-02 00:54:11.897][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-02 00:54:11.937][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-02 00:54:11.969][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 00:54:11.972][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-02 00:54:11.974][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-02 00:54:11.976][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 00:54:11.978][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:11.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:11.983][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:11.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:11.988][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:11.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-02 00:54:12.020][biodb::testContext]
biodb.INFO [2024-03-02 00:54:12.022][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:54:12.025][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-03-02 00:54:12.027][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:54:12.029][biodb::testContext]
biodb.INFO [2024-03-02 00:54:12.034][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:54:12.038][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 00:54:12.047][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:54:12.049][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 00:54:12.052][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 00:54:12.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.061][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 00:54:12.063][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 00:54:12.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.075][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 00:54:12.078][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 00:54:12.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.087][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 00:54:12.089][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 00:54:12.092][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 00:54:12.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.102][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 00:54:12.107][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 00:54:12.110][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 00:54:12.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.118][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 00:54:12.121][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 00:54:12.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.130][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 00:54:12.133][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 00:54:12.137][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 00:54:12.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.146][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 00:54:12.148][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 00:54:12.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.156][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 00:54:12.159][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 00:54:12.161][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 00:54:12.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.171][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[2024-03-02 00:54:12.174][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:54:12.177][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 00:54:12.180][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 00:54:12.182][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 00:54:12.185][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 00:54:12.187][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 00:54:12.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.198][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 00:54:12.200][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 00:54:12.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.210][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 00:54:12.213][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 00:54:12.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.223][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 00:54:12.226][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 00:54:12.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.236][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 00:54:12.239][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 00:54:12.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.250][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 00:54:12.253][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 00:54:12.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.261][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:54:12.265][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 00:54:12.287][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 00:54:12.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.296][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 00:54:12.298][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 00:54:12.301][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 00:54:12.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.311][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 00:54:12.316][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.362][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 00:54:12.365][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:12.370][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.377][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.380][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.383][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:54:12.386][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:12.388][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.390][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 00:54:12.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:12.395][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.399][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.402][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:54:12.402][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:54:12.402][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:54:12.402][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:54:12.402][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:54:12.405][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:12.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:12.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:12.413][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:12.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:12.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:12.422][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.424][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.427][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:12.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:12.433][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.436][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.439][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 00:54:12.445][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.448][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:54:12.453][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.455][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:12.458][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.460][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.465][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.469][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:54:12.472][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:12.475][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.478][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 00:54:12.481][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:12.483][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.487][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.489][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:54:12.489][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:54:12.489][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:54:12.489][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:54:12.489][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:54:12.492][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:12.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:12.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:12.552][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:12.554][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:12.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:12.560][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.562][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.565][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:12.567][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:12.570][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.572][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.575][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 00:54:12.579][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.582][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 00:54:12.584][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.587][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:12.591][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.594][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.596][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.599][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.601][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:54:12.604][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:12.606][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.609][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 00:54:12.612][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:12.615][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.617][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.620][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:12.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:12.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:12.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:12.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:12.636][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:12.638][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.641][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.644][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:12.646][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:12.648][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.650][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.653][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 00:54:12.657][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.659][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:54:12.662][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:12.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.669][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.671][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.673][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.676][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:54:12.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:12.681][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.684][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 00:54:12.688][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:12.690][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.693][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:12.696][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.699][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:12.702][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:12.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:12.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:12.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:12.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:12.716][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:12.719][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.721][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:12.724][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:12.726][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:12.728][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:12.732][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:54:12.735][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:12.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:12.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:12.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:12.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:12.934][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 00:54:12.938][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 00:54:12.941][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 00:54:12.945][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 00:54:12.949][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:54:12.953][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 00:54:12.956][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 00:54:12.960][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 00:54:12.964][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 00:54:12.968][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 00:54:12.972][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:54:12.976][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 00:54:12.979][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 00:54:12.982][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 00:54:12.987][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 00:54:12.990][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:54:12.995][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 00:54:13.002][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 00:54:13.006][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:54:13.011][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 00:54:13.015][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 00:54:13.019][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 00:54:13.024][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 00:54:13.028][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 00:54:13.031][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 00:54:13.035][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 00:54:13.039][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 00:54:13.042][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 00:54:13.046][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 00:54:13.049][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 00:54:13.052][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 00:54:13.056][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 00:54:13.059][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 00:54:13.065][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 00:54:13.072][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 00:54:13.075][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 00:54:13.079][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 00:54:13.083][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 00:54:13.087][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 00:54:13.091][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 00:54:13.094][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 00:54:13.099][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 00:54:13.103][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 00:54:13.107][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 00:54:13.110][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 00:54:13.116][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 00:54:13.120][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 00:54:13.124][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 00:54:13.128][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 00:54:13.132][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 00:54:13.135][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 00:54:13.138][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 00:54:13.142][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 00:54:13.145][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 00:54:13.150][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 00:54:13.153][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 00:54:13.159][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 00:54:13.162][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 00:54:13.165][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 00:54:13.170][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 00:54:13.173][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 00:54:13.177][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 00:54:13.182][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 00:54:13.186][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 00:54:13.189][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 00:54:13.194][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 00:54:13.197][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:54:13.201][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:54:13.205][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 00:54:13.210][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 00:54:13.214][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 00:54:13.217][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 00:54:13.221][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 00:54:13.226][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 00:54:13.248][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 00:54:13.251][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 00:54:13.257][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 00:54:13.263][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 00:54:13.267][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 00:54:13.271][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 00:54:13.275][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 00:54:13.279][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 00:54:13.283][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 00:54:13.287][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 00:54:13.291][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:54:13.295][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:54:13.298][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.302][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.305][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[2024-03-02 00:54:13.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.450][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[2024-03-02 00:54:13.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.537][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[2024-03-02 00:54:13.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:13.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:13.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:13.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:13.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:13.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:13.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:13.571][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-02 00:54:13.574][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:54:13.579][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:13.581][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-02 00:54:13.584][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:13.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:13.589][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:13.591][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:13.593][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:13.596][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:13.598][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:54:13.601][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:13.603][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:13.606][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-02 00:54:13.608][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-02 00:54:13.610][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-02 00:54:13.613][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:13.615][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:54:13.615][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:54:13.618][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:13.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:13.623][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:13.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:13.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:13.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:13.632][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:13.634][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-02 00:54:13.634][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-02 00:54:13.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:13.638][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:13.640][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:13.643][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:13.646][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-02 00:54:13.649][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:54:13.659][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:54:13.661][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-02 00:54:13.664][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:54:13.667][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-02 00:54:13.670][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-02 00:54:13.672][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-02 00:54:13.676][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-02 00:54:13.679][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-02 00:54:13.682][biodb::testThat]
biodb.INFO [2024-03-02 00:54:13.686][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-03-02 00:54:13.688][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:54:13.691][biodb::testThat]
biodb.DEBUG[2024-03-02 00:54:13.703][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-03-02 00:54:13.712][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:54:13.714][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:54:13.718][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-03-02 00:54:14.331][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-03-02 00:54:14.942][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:54:14.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-03-02 00:54:14.956][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-03-02 00:54:15.030][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-03-02 00:54:15.037][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:54:15.040][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:54:15.079][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-03-02 00:54:15.741][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-03-02 00:54:16.376][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:54:16.382][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-03-02 00:54:16.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-03-02 00:54:16.418][biodb::testThat]
biodb.INFO [2024-03-02 00:54:16.420][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-03-02 00:54:16.423][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:54:16.425][biodb::testThat]
biodb.INFO [2024-03-02 00:54:16.487][biodb::testThat]
biodb.INFO [2024-03-02 00:54:16.490][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-03-02 00:54:16.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:54:16.494][biodb::testThat]
biodb.DEBUG[2024-03-02 00:54:16.501][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-02 00:54:16.508][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:54:16.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:54:16.514][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-03-02 00:54:16.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-03-02 00:54:17.430][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:54:17.434][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-03-02 00:54:17.443][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-03-02 00:54:17.456][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-02 00:54:17.463][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:54:17.466][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-03-02 00:54:17.469][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:54:17.472][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-03-02 00:54:17.486][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-03-02 00:54:17.493][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:54:17.496][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-02 00:54:17.498][rule$waitAsNeeded] Wait 0.015182 second(s).
biodb.TRACE[2024-03-02 00:54:17.628][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-03-02 00:54:18.078][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-03-02 00:54:18.549][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:54:18.553][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-03-02 00:54:18.561][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-03-02 00:54:18.578][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-03-02 00:54:18.585][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:54:18.588][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-02 00:54:18.590][rule$waitAsNeeded] Wait 0.0361328 second(s).
biodb.TRACE[2024-03-02 00:54:18.756][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-03-02 00:54:19.970][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-03-02 00:54:21.629][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:54:21.635][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-03-02 00:54:21.716][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-03-02 00:54:22.026][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-03-02 00:54:22.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:54:22.037][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:54:22.042][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-03-02 00:54:23.355][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-03-02 00:54:24.834][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:54:24.838][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-03-02 00:54:24.876][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-03-02 00:54:25.184][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 00:54:25.187][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-02 00:54:25.190][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-02 00:54:25.192][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 00:54:25.196][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:25.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:25.203][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.208][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-02 00:54:25.224][biodb::testContext]
biodb.INFO [2024-03-02 00:54:25.227][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:54:25.229][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-03-02 00:54:25.231][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:54:25.236][biodb::testContext]
biodb.INFO [2024-03-02 00:54:25.241][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:54:25.245][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 00:54:25.255][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:54:25.258][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 00:54:25.261][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 00:54:25.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.272][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 00:54:25.275][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 00:54:25.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.292][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 00:54:25.295][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 00:54:25.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.306][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 00:54:25.310][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 00:54:25.314][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 00:54:25.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.324][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 00:54:25.326][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 00:54:25.329][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 00:54:25.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.338][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 00:54:25.340][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 00:54:25.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.350][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 00:54:25.352][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 00:54:25.357][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 00:54:25.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.366][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 00:54:25.369][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 00:54:25.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.379][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 00:54:25.382][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 00:54:25.384][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 00:54:25.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.395][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:54:25.398][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 00:54:25.400][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 00:54:25.403][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 00:54:25.406][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 00:54:25.408][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 00:54:25.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.417][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 00:54:25.419][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 00:54:25.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.429][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 00:54:25.432][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 00:54:25.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.441][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 00:54:25.446][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 00:54:25.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.456][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 00:54:25.460][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 00:54:25.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.518][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 00:54:25.521][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 00:54:25.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.539][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[2024-03-02 00:54:25.542][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:54:25.544][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 00:54:25.592][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 00:54:25.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.621][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 00:54:25.624][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 00:54:25.626][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 00:54:25.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.633][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 00:54:25.637][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.638][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 00:54:25.640][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.641][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:25.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.645][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.647][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.650][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:54:25.651][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:25.652][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.654][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 00:54:25.656][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:25.659][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.661][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.663][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:54:25.663][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:54:25.663][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:54:25.663][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:54:25.663][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:54:25.664][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:25.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:25.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:25.669][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:25.671][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:25.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:25.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.677][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.679][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:25.680][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:25.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.682][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.684][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 00:54:25.688][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.690][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:54:25.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:25.695][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.696][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.697][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.698][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.700][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:54:25.701][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:25.702][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.704][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 00:54:25.705][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:25.706][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.708][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.710][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:54:25.710][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:54:25.710][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:54:25.710][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:54:25.710][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:54:25.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:25.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:25.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:25.720][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:25.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:25.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:25.727][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.729][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:25.734][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:25.736][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.739][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.742][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 00:54:25.746][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.749][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 00:54:25.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.754][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:25.756][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.759][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.762][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.764][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.767][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:54:25.771][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:25.773][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.776][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 00:54:25.778][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:25.781][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.784][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.787][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.789][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:25.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:25.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:25.795][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:25.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:25.800][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:25.803][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.805][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:25.809][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:25.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.815][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.818][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 00:54:25.822][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.824][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:54:25.827][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:25.832][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.834][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.839][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.842][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.844][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:54:25.847][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:25.850][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.852][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 00:54:25.855][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:25.857][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.860][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:25.863][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.865][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:25.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:25.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:25.874][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:25.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:25.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:25.881][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:25.884][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.886][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:25.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:25.890][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:25.892][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:25.895][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:54:25.897][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.953][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.DEBUG[2024-03-02 00:54:25.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:25.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.988][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[2024-03-02 00:54:25.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:25.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:25.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:25.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:25.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.038][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[2024-03-02 00:54:26.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.078][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 00:54:26.082][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 00:54:26.088][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 00:54:26.092][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 00:54:26.095][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:54:26.100][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 00:54:26.104][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 00:54:26.107][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 00:54:26.111][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 00:54:26.114][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 00:54:26.118][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:54:26.122][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 00:54:26.125][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 00:54:26.128][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 00:54:26.133][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 00:54:26.137][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:54:26.143][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 00:54:26.147][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 00:54:26.150][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:54:26.153][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 00:54:26.157][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 00:54:26.161][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 00:54:26.164][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 00:54:26.169][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 00:54:26.175][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 00:54:26.179][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 00:54:26.184][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 00:54:26.188][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 00:54:26.191][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 00:54:26.195][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 00:54:26.224][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 00:54:26.229][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 00:54:26.233][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 00:54:26.236][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 00:54:26.240][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 00:54:26.244][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 00:54:26.247][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 00:54:26.253][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 00:54:26.256][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 00:54:26.259][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 00:54:26.262][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 00:54:26.269][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 00:54:26.272][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 00:54:26.277][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 00:54:26.281][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 00:54:26.284][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 00:54:26.289][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 00:54:26.293][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 00:54:26.297][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 00:54:26.301][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 00:54:26.307][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 00:54:26.312][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 00:54:26.316][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 00:54:26.319][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 00:54:26.323][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 00:54:26.326][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 00:54:26.330][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 00:54:26.336][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 00:54:26.341][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 00:54:26.344][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 00:54:26.350][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 00:54:26.353][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 00:54:26.357][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 00:54:26.362][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 00:54:26.366][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 00:54:26.370][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 00:54:26.374][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:54:26.378][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:54:26.384][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 00:54:26.390][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 00:54:26.393][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 00:54:26.397][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 00:54:26.401][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 00:54:26.404][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 00:54:26.410][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 00:54:26.414][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 00:54:26.418][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 00:54:26.421][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 00:54:26.424][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 00:54:26.428][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 00:54:26.432][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 00:54:26.435][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 00:54:26.439][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 00:54:26.443][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 00:54:26.447][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:54:26.450][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:54:26.454][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.459][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:54:26.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:26.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:26.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:26.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:26.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:26.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:54:26.768][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-02 00:54:26.772][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:54:26.777][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:26.780][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-02 00:54:26.784][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:26.786][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:54:26.789][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:26.791][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:54:26.793][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:26.795][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:54:26.798][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:54:26.800][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:54:26.802][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:26.804][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-02 00:54:26.806][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-02 00:54:26.808][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-02 00:54:26.811][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 00:54:26.813][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:54:26.813][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:54:26.815][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:54:26.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:26.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:26.822][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:54:26.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:54:26.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:54:26.827][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:54:26.830][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-02 00:54:26.830][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-02 00:54:26.832][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:54:26.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:54:26.836][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 00:54:26.838][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:54:26.841][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-02 00:54:26.845][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:54:26.852][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:54:26.854][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-02 00:54:26.857][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-02 00:54:26.860][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-02 00:54:26.863][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-02 00:54:26.865][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-02 00:54:26.868][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-02 00:54:26.871][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-02 00:54:26.874][biodb::testThat]
biodb.INFO [2024-03-02 00:54:26.876][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-03-02 00:54:26.878][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:54:26.880][biodb::testThat]
biodb.DEBUG[2024-03-02 00:54:26.888][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-02 00:54:26.898][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:54:26.902][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-03-02 00:54:26.905][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:54:26.976][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-03-02 00:54:28.862][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-03-02 00:54:28.865][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-02 00:54:28.869][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-03-02 00:54:28.872][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-03-02 00:54:28.877][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-03-02 00:54:28.880][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:54:28.883][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-02 00:54:28.886][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-02 00:54:28.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:54:28.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:28.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:28.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:28.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:28.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:28.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:54:28.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:28.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:28.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:28.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:28.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:28.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:28.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:28.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:28.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:28.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:28.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:28.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:28.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:28.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:28.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:28.964][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:54:28.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:54:28.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:28.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:28.975][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:54:28.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:54:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:28.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:28.985][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:28.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:28.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:28.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:28.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.006][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.026][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:54:29.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.037][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:54:29.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:29.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:29.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.058][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:29.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:29.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.086][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:54:29.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.096][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-02 00:54:29.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.124][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:54:29.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.164][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.169][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.179][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:54:29.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:54:29.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:29.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:29.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:29.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:29.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:29.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:54:29.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:54:29.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-02 00:54:29.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:54:29.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:54:29.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.317][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.338][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.348][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:54:29.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.358][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-02 00:54:29.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:29.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:29.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.378][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:29.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:29.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.409][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:54:29.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.420][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-02 00:54:29.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.474][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-02 00:54:29.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.484][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.494][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.518][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:54:29.627][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-03-02 00:54:29.634][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:54:29.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:54:29.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:29.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:29.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:29.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:29.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:29.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:54:29.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:54:29.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:54:29.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:54:29.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:54:29.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.690][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 00:54:29.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 00:54:29.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.700][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 00:54:29.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 00:54:29.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.710][private$selectFields] Fields none
biodb.TRACE[2024-03-02 00:54:29.712][private$selectFields]
biodb.TRACE[2024-03-02 00:54:29.714][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-02 00:54:29.716][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:54:29.720][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:54:29.722][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.725][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.730][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.732][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.735][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.739][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.742][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.744][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.749][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.752][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.756][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.760][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.763][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.766][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.771][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.774][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:29.776][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:29.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.782][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.784][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.787][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.792][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.795][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.797][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.802][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.805][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.807][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.813][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.816][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.820][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.825][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.827][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.831][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.836][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.839][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.841][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.847][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.850][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.852][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.858][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.860][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:29.863][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:29.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.868][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.871][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.874][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.879][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.882][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.886][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.891][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.894][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:54:29.896][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:54:29.898][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.901][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.913][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.916][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.919][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:29.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.925][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.928][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.930][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:29.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.935][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.938][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.940][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:29.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.944][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.946][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.949][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:29.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.953][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.955][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:29.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:29.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.963][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.965][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:29.967][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:29.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.973][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.976][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.979][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:29.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:29.986][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:29.990][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-03-02 00:54:29.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:29.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:29.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:30.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:30.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:30.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:30.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.052][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.062][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.073][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.123][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.218][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.228][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.238][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.261][private$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[2024-03-02 00:54:30.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:54:30.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:30.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:30.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:30.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:30.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:30.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:54:30.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:54:30.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:54:30.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:54:30.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:54:30.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.319][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 00:54:30.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 00:54:30.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.329][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 00:54:30.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 00:54:30.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.338][private$selectFields] Fields none
biodb.TRACE[2024-03-02 00:54:30.340][private$selectFields]
biodb.TRACE[2024-03-02 00:54:30.342][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-02 00:54:30.344][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:54:30.346][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:54:30.348][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:30.350][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:30.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.354][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.362][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.364][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.366][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.370][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.373][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.376][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.381][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.383][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.386][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.390][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.393][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.396][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.400][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.403][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.405][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.410][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.412][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.415][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.420][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.422][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:30.424][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:30.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.428][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.431][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.433][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.437][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.440][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.442][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.446][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.448][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.451][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.455][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.457][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.459][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.464][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.466][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.469][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.473][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.475][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.478][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.483][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.486][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.489][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.494][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.496][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:54:30.499][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-02 00:54:30.501][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:30.504][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:30.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.509][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.515][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.520][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.522][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.525][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.531][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.533][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.536][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.541][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.544][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.547][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.551][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.553][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.560][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.562][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.565][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.570][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.572][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.575][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.580][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.583][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-03-02 00:54:30.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:30.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:30.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:30.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:30.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:54:30.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:54:30.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:54:30.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.650][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.661][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.671][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-02 00:54:30.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.707][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-02 00:54:30.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:54:30.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:54:30.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:54:30.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:54:30.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:54:30.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.843][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.854][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.866][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-02 00:54:30.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:54:30.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:54:30.887][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-03-02 00:54:30.889][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:54:30.892][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-03-02 00:54:30.908][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 00:54:30.911][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-02 00:54:30.914][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-02 00:54:30.916][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 00:54:30.918][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:54:30.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:54:30.922][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:54:30.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:54:30.926][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:54:30.929][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".
[ 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
LipidmapsStructureConn 4.527 1.95824.688
LipidmapsStructureEntry0.8510.0321.843