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This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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Package 200/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_19
git_last_commit: fad38a4
git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024)
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbChebi on kjohnson3


To the developers/maintainers of the biodbChebi package:
- 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: biodbChebi
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz
StartedAt: 2024-05-06 19:58:51 -0400 (Mon, 06 May 2024)
EndedAt: 2024-05-06 19:59:19 -0400 (Mon, 06 May 2024)
EllapsedTime: 27.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbChebi.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/biodbChebi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 14 | WARN 0 | SKIP 0 | PASS 129 ]
  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-mac-arm64/meat/biodbChebi.Rcheck/00check.log’
for details.

Installation output

biodbChebi.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** 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 (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-05-06 19:59:12.312][biodb::testContext]
biodb.INFO [2024-05-06 19:59:12.313][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:12.314][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-06 19:59:12.314][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:12.314][biodb::testContext]
biodb.INFO [2024-05-06 19:59:12.317][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:12.318][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:12.321][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:12.322][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-06 19:59:12.322][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-06 19:59:12.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.323][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-06 19:59:12.330][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-06 19:59:12.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.331][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-06 19:59:12.331][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-06 19:59:12.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.332][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-06 19:59:12.332][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-06 19:59:12.338][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-06 19:59:12.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.338][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[2024-05-06 19:59:12.339][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-06 19:59:12.339][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-06 19:59:12.339][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-06 19:59:12.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.340][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-06 19:59:12.340][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-06 19:59:12.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.341][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-06 19:59:12.342][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-06 19:59:12.342][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-06 19:59:12.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.343][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-06 19:59:12.343][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-06 19:59:12.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.344][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-06 19:59:12.344][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-06 19:59:12.344][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-06 19:59:12.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.345][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:12.346][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-06 19:59:12.346][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-06 19:59:12.346][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-06 19:59:12.346][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-06 19:59:12.347][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-06 19:59:12.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.348][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-06 19:59:12.348][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-06 19:59:12.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.349][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-06 19:59:12.349][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-06 19:59:12.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.350][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-06 19:59:12.350][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-06 19:59:12.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.351][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-06 19:59:12.351][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-06 19:59:12.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.352][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-06 19:59:12.353][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-06 19:59:12.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.354][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:12.354][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-06 19:59:12.360][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-06 19:59:12.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.361][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-06 19:59:12.361][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-06 19:59:12.361][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-06 19:59:12.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.364][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-06 19:59:12.375][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.380][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-06 19:59:12.380][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.381][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:12.381][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.381][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.381][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.382][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.382][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:12.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:12.382][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.383][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-06 19:59:12.383][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:12.383][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.383][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.384][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:12.384][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:12.384][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:12.384][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:12.384][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:12.384][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:12.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:12.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.385][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.386][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:12.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:12.386][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.387][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.387][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-06 19:59:12.387][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.388][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:12.388][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.388][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:12.389][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.389][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.389][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.390][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:12.390][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:12.390][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.390][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-06 19:59:12.391][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:12.391][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.391][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.391][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:12.391][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:12.391][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:12.391][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:12.391][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:12.392][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:12.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.392][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:12.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.393][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.394][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:12.394][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:12.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.394][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.395][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-06 19:59:12.395][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.395][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-06 19:59:12.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:12.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.397][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.400][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.401][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:12.401][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:12.401][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.401][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-06 19:59:12.402][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:12.402][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.402][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.402][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.403][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:12.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.403][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:12.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.404][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.404][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.405][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:12.405][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:12.405][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.405][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.406][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-06 19:59:12.406][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.406][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:12.407][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.407][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:12.407][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.408][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.408][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.408][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.408][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:12.409][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:12.409][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.409][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-06 19:59:12.409][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:12.410][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.410][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.410][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.410][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:12.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.411][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:12.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.412][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.412][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.412][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:12.413][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:12.413][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.413][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:12.415][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:12.415][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.416][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[2024-05-06 19:59:12.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.422][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[2024-05-06 19:59:12.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.426][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[2024-05-06 19:59:12.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.427][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[2024-05-06 19:59:12.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.435][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-06 19:59:12.438][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-06 19:59:12.438][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-06 19:59:12.439][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-06 19:59:12.439][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:12.439][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-06 19:59:12.440][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:12.440][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:12.440][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-06 19:59:12.441][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-06 19:59:12.441][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:12.442][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-06 19:59:12.442][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:12.442][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:12.443][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-06 19:59:12.443][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:12.443][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-06 19:59:12.444][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-06 19:59:12.444][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:12.445][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-06 19:59:12.445][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-06 19:59:12.445][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-06 19:59:12.446][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-06 19:59:12.446][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-06 19:59:12.446][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-06 19:59:12.447][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-06 19:59:12.447][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-06 19:59:12.448][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-06 19:59:12.448][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-06 19:59:12.448][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-06 19:59:12.449][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-06 19:59:12.449][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-06 19:59:12.449][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-06 19:59:12.450][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-06 19:59:12.450][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-06 19:59:12.451][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-06 19:59:12.451][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-06 19:59:12.451][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-06 19:59:12.452][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-06 19:59:12.452][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-06 19:59:12.452][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-06 19:59:12.453][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-06 19:59:12.453][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-06 19:59:12.456][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-06 19:59:12.456][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-06 19:59:12.457][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-06 19:59:12.457][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-06 19:59:12.457][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-06 19:59:12.458][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-06 19:59:12.458][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-06 19:59:12.458][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-06 19:59:12.459][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-06 19:59:12.459][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-06 19:59:12.459][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-06 19:59:12.460][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-06 19:59:12.460][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-06 19:59:12.461][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-06 19:59:12.461][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-06 19:59:12.461][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-06 19:59:12.462][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-06 19:59:12.462][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-06 19:59:12.462][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-06 19:59:12.463][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-06 19:59:12.463][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-06 19:59:12.463][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-06 19:59:12.464][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-06 19:59:12.464][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:12.464][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:12.465][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-06 19:59:12.465][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-06 19:59:12.466][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-06 19:59:12.466][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-06 19:59:12.466][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-06 19:59:12.467][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-06 19:59:12.467][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-06 19:59:12.467][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-06 19:59:12.468][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-06 19:59:12.468][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-06 19:59:12.469][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-06 19:59:12.469][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-06 19:59:12.469][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-06 19:59:12.470][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-06 19:59:12.470][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-06 19:59:12.472][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-06 19:59:12.473][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:12.474][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:12.474][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.475][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.475][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[2024-05-06 19:59:12.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.484][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[2024-05-06 19:59:12.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.498][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[2024-05-06 19:59:12.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:12.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:12.503][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:12.509][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-06 19:59:12.509][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.509][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.510][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.510][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:12.510][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.511][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.511][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.511][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-06 19:59:12.511][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-06 19:59:12.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:12.512][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.512][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-06 19:59:12.512][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:12.513][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-06 19:59:12.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.514][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:12.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:12.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:12.515][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:12.515][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-06 19:59:12.515][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-06 19:59:12.515][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:12.516][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:12.516][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:12.516][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-06 19:59:12.516][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-06 19:59:12.518][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:12.519][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:12.519][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-06 19:59:12.519][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:12.520][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:12.520][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:12.531][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-06 19:59:12.531][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-06 19:59:12.533][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-06 19:59:12.535][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-06 19:59:12.536][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-06 19:59:12.537][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-06 19:59:12.537][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-06 19:59:12.537][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-06 19:59:12.542][biodb::testThat]
biodb.INFO [2024-05-06 19:59:12.542][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-06 19:59:12.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:12.542][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:12.544][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-05-06 19:59:12.545][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-06 19:59:12.546][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-06 19:59:12.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:12.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.556][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.TRACE[2024-05-06 19:59:12.560][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.561][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.561][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.567][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.567][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.567][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.576][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.577][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.577][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.578][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.583][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.583][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.584][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.586][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.588][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.589][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.590][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:12.590][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.591][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.592][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.592][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.592][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.594][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.594][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.595][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.596][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:12.596][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.597][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.597][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:12.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.598][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.598][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.599][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:12.621][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-05-06 19:59:12.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:12.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:12.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.650][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:12.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:12.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.651][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:12.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:12.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.652][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:12.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:12.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.685][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.685][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.686][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.696][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.697][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.705][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.705][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.706][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.713][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.713][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.714][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.721][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.721][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.722][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.729][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.729][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.733][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.734][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.735][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.736][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.739][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.739][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.739][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.743][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.744][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.745][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.746][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.746][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.746][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.747][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.750][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.751][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.752][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.753][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.754][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.754][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.754][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.758][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.759][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.760][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.761][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.761][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.762][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.762][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.769][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.769][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.776][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.776][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.777][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.781][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.781][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.781][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.785][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.785][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.786][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.787][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.788][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.788][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.790][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.790][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.790][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.792][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.792][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.793][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.794][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.794][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.795][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.796][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.796][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.797][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.798][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.799][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.799][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.801][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.801][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.801][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.803][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.804][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.805][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.805][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.806][ef$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:12.808][biodb::testThat]
biodb.INFO [2024-05-06 19:59:12.808][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-06 19:59:12.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:12.809][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:12.813][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-05-06 19:59:12.817][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-06 19:59:12.818][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-05-06 19:59:12.819][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:12.819][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-05-06 19:59:12.819][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:12.827][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-06 19:59:12.827][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-06 19:59:12.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:12.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:12.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:12.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:12.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:12.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:12.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:12.831][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.832][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.832][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.841][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:12.842][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:12.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.842][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.843][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:12.843][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:12.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.844][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.844][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:12.844][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:12.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.845][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.845][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.846][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:12.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.846][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.846][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.847][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:12.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.848][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:12.848][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:12.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.848][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.849][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.849][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:12.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.849][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.850][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.850][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.851][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.851][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:12.851][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:12.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.852][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.852][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:12.852][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:12.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.853][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:12.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:12.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:12.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:12.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:12.863][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-06 19:59:12.864][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-06 19:59:12.871][biodb::testThat]
biodb.INFO [2024-05-06 19:59:12.871][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-06 19:59:12.871][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:12.872][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:12.873][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:12.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:12.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:12.873][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:12.874][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.INFO [2024-05-06 19:59:12.962][biodb::testThat]
biodb.INFO [2024-05-06 19:59:12.963][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-06 19:59:12.963][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:12.963][biodb::testThat]
biodb.INFO [2024-05-06 19:59:12.983][biodb::testThat]
biodb.INFO [2024-05-06 19:59:12.984][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-06 19:59:12.984][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:12.984][biodb::testThat]
biodb.INFO [2024-05-06 19:59:13.002][biodb::testThat]
biodb.INFO [2024-05-06 19:59:13.003][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-06 19:59:13.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:13.003][biodb::testThat]
biodb.INFO [2024-05-06 19:59:13.006][biodb::testThat]
biodb.INFO [2024-05-06 19:59:13.006][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-06 19:59:13.009][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:13.009][biodb::testThat]
biodb.INFO [2024-05-06 19:59:13.012][biodb::testThat]
biodb.INFO [2024-05-06 19:59:13.012][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-06 19:59:13.013][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:13.013][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:13.014][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-05-06 19:59:13.473][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-05-06 19:59:14.186][biodb::testThat]
biodb.INFO [2024-05-06 19:59:14.186][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-06 19:59:14.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:14.187][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:14.573][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-05-06 19:59:14.969][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:14.969][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:14.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:14.970][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:14.970][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:14.970][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:14.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:14.971][ef$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:14.971][biodb::testThat]
biodb.INFO [2024-05-06 19:59:14.972][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-06 19:59:14.972][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:14.972][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.001][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.001][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-06 19:59:15.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.002][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.010][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.011][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-06 19:59:15.011][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.011][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.016][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.017][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-06 19:59:15.017][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.017][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.089][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.089][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-06 19:59:15.090][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.090][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:15.090][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-06 19:59:15.104][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-06 19:59:15.109][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-06 19:59:15.109][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.110][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2024-05-06 19:59:15.110][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:15.111][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-06 19:59:15.111][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-06 19:59:15.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:15.115][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.116][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.116][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.118][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:15.118][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:15.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.119][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:15.119][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:15.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.120][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.120][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:15.120][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:15.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.121][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.121][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.121][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.122][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.122][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.122][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.123][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.123][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:15.124][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:15.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.124][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.125][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.125][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.125][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:15.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:15.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.126][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.126][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:15.127][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:15.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.127][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.128][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:15.128][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:15.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.128][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:15.139][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-06 19:59:15.139][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-06 19:59:15.146][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.146][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-06 19:59:15.146][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.146][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:15.150][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-05-06 19:59:15.151][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-05-06 19:59:15.151][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-06 19:59:15.151][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-05-06 19:59:15.152][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-05-06 19:59:15.153][loadFileContents] Loaded 3 files from cache: [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2024-05-06 19:59:15.154][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:15.154][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-05-06 19:59:15.155][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-05-06 19:59:15.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:15.159][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.160][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.162][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:15.162][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:15.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.162][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.163][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:15.163][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:15.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.164][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.164][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:15.164][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:15.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.165][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.165][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.166][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.166][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.166][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.167][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.167][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.168][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:15.168][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:15.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.168][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.169][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.169][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.170][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.170][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:15.170][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:15.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.171][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.171][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:15.171][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:15.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.172][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.172][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:15.173][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:15.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.173][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:15.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:15.185][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.186][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.186][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.188][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:15.188][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:15.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.189][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.189][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:15.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:15.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.190][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:15.190][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:15.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.191][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.191][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:15.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:15.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:15.193][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:15.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.193][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.194][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:15.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:15.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.195][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.195][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.196][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.200][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.200][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.200][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.201][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.202][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:15.202][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:15.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.202][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.203][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:15.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:15.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.204][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.204][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.204][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.206][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:15.206][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:15.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.206][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:15.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:15.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.208][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:15.208][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:15.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.209][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.209][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:15.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:15.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.210][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:15.210][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:15.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.211][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:15.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:15.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:15.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:15.223][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.223][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.224][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.225][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:15.226][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:15.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.226][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.226][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:15.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.228][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:15.228][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:15.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.228][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:15.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:15.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.230][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:15.230][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:15.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.230][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:15.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:15.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.232][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.232][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.232][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.234][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.234][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.235][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.235][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.236][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:15.236][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:15.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.237][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.237][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:15.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:15.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.238][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.238][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.239][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.240][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:15.241][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:15.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.241][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:15.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:15.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.243][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:15.243][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:15.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.243][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.244][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:15.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:15.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.245][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:15.245][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:15.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.245][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.246][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:15.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:15.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:15.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:15.263][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-05-06 19:59:15.264][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-06 19:59:15.264][function(conn, opt)] Entries: [4]: "NULL, NULL, <environment>, <environment>"
biodb.INFO [2024-05-06 19:59:15.277][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.277][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-06 19:59:15.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.278][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.293][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.293][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-06 19:59:15.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.294][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.296][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.297][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-06 19:59:15.297][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.297][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:15.299][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-06 19:59:15.306][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.306][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-06 19:59:15.306][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.307][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-06 19:59:15.317][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.318][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2024-05-06 19:59:15.318][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.319][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2024-05-06 19:59:15.323][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:15.324][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:15.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.324][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.324][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.325][ef$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:15.326][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.326][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-06 19:59:15.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.327][biodb::testThat]
biodb.ERROR[2024-05-06 19:59:15.348][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-06 19:59:15.353][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-06 19:59:15.357][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-06 19:59:15.357][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-06 19:59:15.358][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-06 19:59:15.358][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-06 19:59:15.358][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.359][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.359][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-06 19:59:15.362][biodb::testContext]
biodb.INFO [2024-05-06 19:59:15.363][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:15.363][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-05-06 19:59:15.363][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:15.364][biodb::testContext]
biodb.INFO [2024-05-06 19:59:15.364][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:15.365][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:15.366][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.367][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-06 19:59:15.367][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.368][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-06 19:59:15.368][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.369][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-06 19:59:15.369][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.370][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[2024-05-06 19:59:15.370][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-06 19:59:15.370][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-06 19:59:15.371][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.372][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-06 19:59:15.372][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-06 19:59:15.372][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.373][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-06 19:59:15.373][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.374][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-06 19:59:15.375][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-06 19:59:15.375][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-06 19:59:15.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.376][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-06 19:59:15.376][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.377][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-06 19:59:15.377][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-06 19:59:15.377][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.378][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:15.379][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-06 19:59:15.379][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-06 19:59:15.379][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-06 19:59:15.379][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-06 19:59:15.380][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-06 19:59:15.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.381][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-06 19:59:15.381][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-06 19:59:15.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.382][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-06 19:59:15.382][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-06 19:59:15.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.383][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-06 19:59:15.383][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.384][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-06 19:59:15.384][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-06 19:59:15.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.385][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-06 19:59:15.386][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-06 19:59:15.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.387][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:15.387][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-06 19:59:15.393][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-06 19:59:15.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.394][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-06 19:59:15.394][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-06 19:59:15.394][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-06 19:59:15.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.395][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-06 19:59:15.396][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.396][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-06 19:59:15.397][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.397][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.398][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.398][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.398][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:15.398][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.399][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.399][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-06 19:59:15.399][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.399][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.400][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.400][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.400][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.400][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.400][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:15.400][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:15.400][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.401][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.401][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.402][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.402][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.402][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.402][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.403][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.403][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.403][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-06 19:59:15.404][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.404][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:15.404][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.405][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.405][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.405][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.405][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.406][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.406][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:15.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.406][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.407][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-06 19:59:15.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.407][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.407][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.408][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.408][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.408][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.408][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:15.408][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:15.408][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.409][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.409][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.409][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.410][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.410][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.410][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.411][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-06 19:59:15.411][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.411][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-06 19:59:15.412][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.412][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.412][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.413][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.413][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.413][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.413][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:15.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.414][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.414][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-06 19:59:15.414][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.415][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.415][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.415][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.415][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.416][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.417][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.417][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.417][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.417][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.418][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.418][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.418][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-06 19:59:15.419][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.419][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:15.419][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.419][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.420][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.420][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.420][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.421][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:15.421][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.421][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.421][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-06 19:59:15.422][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.422][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.425][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.425][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.426][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.426][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.426][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.427][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.427][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.428][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.428][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.428][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.428][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.429][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.429][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.439][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[2024-05-06 19:59:15.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.448][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-06 19:59:15.449][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-06 19:59:15.449][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-06 19:59:15.449][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-06 19:59:15.450][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:15.450][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-06 19:59:15.451][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:15.451][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:15.451][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-06 19:59:15.452][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-06 19:59:15.452][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:15.453][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-06 19:59:15.453][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:15.453][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:15.454][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-06 19:59:15.454][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:15.454][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-06 19:59:15.455][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-06 19:59:15.455][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:15.455][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-06 19:59:15.456][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-06 19:59:15.456][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-06 19:59:15.457][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-06 19:59:15.457][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-06 19:59:15.457][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-06 19:59:15.458][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-06 19:59:15.458][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-06 19:59:15.458][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-06 19:59:15.459][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-06 19:59:15.459][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-06 19:59:15.460][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-06 19:59:15.460][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-06 19:59:15.460][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-06 19:59:15.461][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-06 19:59:15.461][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-06 19:59:15.461][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-06 19:59:15.462][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-06 19:59:15.462][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-06 19:59:15.463][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-06 19:59:15.463][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-06 19:59:15.463][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-06 19:59:15.464][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-06 19:59:15.464][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-06 19:59:15.464][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-06 19:59:15.465][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-06 19:59:15.465][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-06 19:59:15.465][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-06 19:59:15.466][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-06 19:59:15.466][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-06 19:59:15.467][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-06 19:59:15.467][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-06 19:59:15.467][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-06 19:59:15.468][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-06 19:59:15.468][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-06 19:59:15.468][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-06 19:59:15.469][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-06 19:59:15.469][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-06 19:59:15.469][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-06 19:59:15.470][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-06 19:59:15.470][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-06 19:59:15.471][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-06 19:59:15.471][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-06 19:59:15.471][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-06 19:59:15.472][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-06 19:59:15.472][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-06 19:59:15.472][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-06 19:59:15.473][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:15.473][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:15.473][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-06 19:59:15.474][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-06 19:59:15.474][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-06 19:59:15.475][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-06 19:59:15.475][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-06 19:59:15.475][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-06 19:59:15.476][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-06 19:59:15.476][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-06 19:59:15.476][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-06 19:59:15.477][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-06 19:59:15.477][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-06 19:59:15.478][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-06 19:59:15.478][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-06 19:59:15.478][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-06 19:59:15.479][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-06 19:59:15.479][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-06 19:59:15.480][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:15.480][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.480][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.481][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.484][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[2024-05-06 19:59:15.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.493][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[2024-05-06 19:59:15.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.498][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[2024-05-06 19:59:15.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.506][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[2024-05-06 19:59:15.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.507][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[2024-05-06 19:59:15.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.511][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:15.514][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.515][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.515][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.516][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.516][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.516][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.516][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.517][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.517][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-06 19:59:15.517][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-06 19:59:15.517][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.518][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.518][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-06 19:59:15.518][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.519][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-06 19:59:15.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.520][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.521][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-06 19:59:15.521][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-06 19:59:15.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.522][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.522][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-06 19:59:15.522][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-06 19:59:15.522][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:15.523][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:15.523][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-06 19:59:15.524][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:15.524][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:15.528][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:15.529][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.529][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-06 19:59:15.529][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.530][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-06 19:59:15.530][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-06 19:59:15.531][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-06 19:59:15.531][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-06 19:59:15.531][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-06 19:59:15.532][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.532][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-05-06 19:59:15.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.532][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:15.534][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-06 19:59:15.535][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.536][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-06 19:59:15.536][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.536][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-06 19:59:15.538][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.539][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.539][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-06 19:59:15.539][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.542][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-06 19:59:15.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.553][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.554][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-06 19:59:15.555][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.556][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-06 19:59:15.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.571][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.572][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.572][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-06 19:59:15.573][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.573][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-06 19:59:15.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.578][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.579][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.579][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-06 19:59:15.579][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.580][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-06 19:59:15.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.588][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.589][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.589][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-06 19:59:15.590][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.590][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-06 19:59:15.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.594][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.595][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.596][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-06 19:59:15.596][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.597][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-06 19:59:15.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.601][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.602][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.602][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-05-06 19:59:15.602][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.603][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-05-06 19:59:15.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-06 19:59:15.609][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.610][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-05-06 19:59:15.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.610][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:15.611][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.613][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.613][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2024-05-06 19:59:15.614][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.614][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2024-05-06 19:59:15.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.619][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.620][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2024-05-06 19:59:15.621][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.622][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2024-05-06 19:59:15.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-06 19:59:15.627][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-06 19:59:15.627][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-06 19:59:15.627][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-06 19:59:15.628][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-06 19:59:15.628][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.628][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.629][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-06 19:59:15.630][biodb::testContext]
biodb.INFO [2024-05-06 19:59:15.631][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:15.631][biodb::testContext] Test context - Test web services
biodb.INFO [2024-05-06 19:59:15.631][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:15.631][biodb::testContext]
biodb.INFO [2024-05-06 19:59:15.632][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:15.633][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:15.634][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.635][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-06 19:59:15.635][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.636][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-06 19:59:15.636][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.637][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-06 19:59:15.637][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.638][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-06 19:59:15.638][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-06 19:59:15.639][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.640][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-06 19:59:15.640][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-06 19:59:15.640][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.641][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-06 19:59:15.641][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.642][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-06 19:59:15.642][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-06 19:59:15.643][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-06 19:59:15.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.644][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-06 19:59:15.644][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.645][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-06 19:59:15.645][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-06 19:59:15.645][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.646][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:15.646][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-06 19:59:15.647][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-06 19:59:15.647][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-06 19:59:15.647][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-06 19:59:15.648][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-06 19:59:15.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.648][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-06 19:59:15.649][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-06 19:59:15.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.650][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-06 19:59:15.650][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-06 19:59:15.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.651][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-06 19:59:15.651][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.652][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[2024-05-06 19:59:15.652][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-06 19:59:15.652][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-06 19:59:15.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.653][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-06 19:59:15.653][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-06 19:59:15.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.654][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:15.654][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-06 19:59:15.659][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-06 19:59:15.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.663][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-06 19:59:15.663][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-06 19:59:15.664][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-06 19:59:15.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.665][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-06 19:59:15.665][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.666][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-06 19:59:15.666][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.667][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.667][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.667][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.667][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:15.668][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.668][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.668][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-06 19:59:15.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.669][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.669][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.669][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.669][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.669][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.669][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:15.669][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:15.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.670][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.671][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.671][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.671][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.671][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.672][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.672][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.672][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-06 19:59:15.673][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.673][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:15.673][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.673][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.674][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.674][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.674][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.674][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.675][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:15.675][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.675][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.675][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-06 19:59:15.676][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.676][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.676][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.676][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.676][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.676][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.676][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:15.676][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:15.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.677][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.678][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.678][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.678][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.679][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.679][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.679][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.680][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-06 19:59:15.680][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.680][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-06 19:59:15.681][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.681][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.681][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.681][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.682][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.682][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.682][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:15.682][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.683][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.683][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-06 19:59:15.683][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.683][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.684][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.684][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.684][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.685][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.686][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.686][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.686][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.686][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.687][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.687][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-06 19:59:15.687][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.688][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:15.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.688][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.689][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.689][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.689][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.690][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:15.690][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.690][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.690][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-06 19:59:15.691][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.691][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.691][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.691][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.692][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.692][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.693][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.693][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.693][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.694][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.694][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.694][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.694][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.695][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.695][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.710][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[2024-05-06 19:59:15.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.714][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-06 19:59:15.715][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-06 19:59:15.715][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-06 19:59:15.715][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-06 19:59:15.716][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:15.716][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-06 19:59:15.717][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:15.717][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:15.717][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-06 19:59:15.718][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-06 19:59:15.718][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:15.718][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-06 19:59:15.719][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:15.719][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:15.719][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-06 19:59:15.720][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:15.720][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-06 19:59:15.721][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-06 19:59:15.721][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:15.721][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-06 19:59:15.722][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-06 19:59:15.722][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-06 19:59:15.722][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-06 19:59:15.723][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-06 19:59:15.723][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-06 19:59:15.724][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-06 19:59:15.724][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-06 19:59:15.724][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-06 19:59:15.725][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-06 19:59:15.725][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-06 19:59:15.725][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-06 19:59:15.726][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-06 19:59:15.726][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-06 19:59:15.727][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-06 19:59:15.727][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-06 19:59:15.727][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-06 19:59:15.728][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-06 19:59:15.728][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-06 19:59:15.728][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-06 19:59:15.729][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-06 19:59:15.729][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-06 19:59:15.729][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-06 19:59:15.730][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-06 19:59:15.730][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-06 19:59:15.731][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-06 19:59:15.731][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-06 19:59:15.731][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-06 19:59:15.732][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-06 19:59:15.732][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-06 19:59:15.732][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-06 19:59:15.733][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-06 19:59:15.733][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-06 19:59:15.734][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-06 19:59:15.734][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-06 19:59:15.734][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-06 19:59:15.735][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-06 19:59:15.735][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-06 19:59:15.735][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-06 19:59:15.736][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-06 19:59:15.736][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-06 19:59:15.736][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-06 19:59:15.737][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-06 19:59:15.737][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-06 19:59:15.737][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-06 19:59:15.738][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-06 19:59:15.738][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-06 19:59:15.739][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:15.739][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:15.739][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-06 19:59:15.740][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-06 19:59:15.740][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-06 19:59:15.740][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-06 19:59:15.741][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-06 19:59:15.741][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-06 19:59:15.741][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-06 19:59:15.742][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-06 19:59:15.742][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-06 19:59:15.743][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-06 19:59:15.743][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-06 19:59:15.743][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-06 19:59:15.744][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-06 19:59:15.744][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-06 19:59:15.744][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-06 19:59:15.745][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-06 19:59:15.745][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:15.746][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.746][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.746][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.748][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[2024-05-06 19:59:15.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.760][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[2024-05-06 19:59:15.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.776][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:15.776][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.777][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.777][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.777][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.777][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.778][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.778][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.778][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-06 19:59:15.779][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-06 19:59:15.779][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.779][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.779][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-06 19:59:15.780][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.781][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.781][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.781][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.781][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-06 19:59:15.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.781][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.782][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.782][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-06 19:59:15.782][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-06 19:59:15.783][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.783][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.783][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-06 19:59:15.783][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-06 19:59:15.784][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:15.784][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:15.785][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-06 19:59:15.785][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:15.786][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:15.786][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:15.787][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.787][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-06 19:59:15.788][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.788][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-06 19:59:15.788][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-06 19:59:15.789][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-06 19:59:15.789][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-06 19:59:15.789][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-06 19:59:15.790][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.790][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-05-06 19:59:15.790][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.790][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:15.791][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-06 19:59:15.793][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.793][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-06 19:59:15.793][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.794][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-06 19:59:15.795][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.797][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.797][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-06 19:59:15.797][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.798][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2024-05-06 19:59:15.801][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-06 19:59:15.801][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-06 19:59:15.802][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-06 19:59:15.802][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-06 19:59:15.802][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.803][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.803][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-06 19:59:15.804][biodb::testContext]
biodb.INFO [2024-05-06 19:59:15.805][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:15.805][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-05-06 19:59:15.805][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:15.805][biodb::testContext]
biodb.INFO [2024-05-06 19:59:15.806][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:15.807][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:15.808][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.808][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-06 19:59:15.809][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.810][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-06 19:59:15.810][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.811][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-06 19:59:15.811][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.812][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-06 19:59:15.812][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-06 19:59:15.813][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.814][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-06 19:59:15.814][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-06 19:59:15.814][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.815][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-06 19:59:15.815][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.816][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-06 19:59:15.816][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-06 19:59:15.817][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-06 19:59:15.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.818][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-06 19:59:15.818][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.819][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-06 19:59:15.819][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-06 19:59:15.819][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-06 19:59:15.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.820][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:15.820][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-06 19:59:15.821][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-06 19:59:15.821][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-06 19:59:15.821][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-06 19:59:15.821][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-06 19:59:15.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.822][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-06 19:59:15.823][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-06 19:59:15.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.824][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-06 19:59:15.824][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-06 19:59:15.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.825][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-06 19:59:15.825][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-06 19:59:15.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.826][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-06 19:59:15.826][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-06 19:59:15.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.827][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-06 19:59:15.827][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-06 19:59:15.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.828][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:15.829][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-06 19:59:15.833][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-06 19:59:15.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.834][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-06 19:59:15.834][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-06 19:59:15.835][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-06 19:59:15.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.836][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-06 19:59:15.836][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.836][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-06 19:59:15.837][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.837][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.838][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.838][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.838][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.838][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:15.839][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.839][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.839][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-06 19:59:15.839][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.840][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.840][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.840][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.840][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.840][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.840][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:15.840][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:15.840][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.841][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.842][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.842][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.842][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.843][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.843][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.843][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.843][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-06 19:59:15.844][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.844][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:15.844][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.845][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.845][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.846][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.846][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.846][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:15.846][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.847][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.847][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-06 19:59:15.847][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.847][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.847][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.848][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.848][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.848][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.848][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:15.848][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:15.848][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.848][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.849][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.849][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.850][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.850][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.850][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.850][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.851][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.851][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-06 19:59:15.851][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.852][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-06 19:59:15.852][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.852][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.853][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.853][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.853][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.853][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.854][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:15.854][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.854][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.854][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-06 19:59:15.855][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.855][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.855][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.855][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.856][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.856][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.857][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.857][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.857][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.858][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.858][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.858][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.858][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-06 19:59:15.859][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.859][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:15.860][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.860][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.860][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.860][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.861][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.861][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.861][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:15.861][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.862][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.862][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-06 19:59:15.862][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.862][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.863][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.863][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.863][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:15.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.864][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.864][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.865][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.867][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.868][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.868][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.868][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:15.869][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.869][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.882][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[2024-05-06 19:59:15.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.888][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-06 19:59:15.888][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-06 19:59:15.889][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-06 19:59:15.889][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-06 19:59:15.890][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:15.890][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-06 19:59:15.890][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:15.891][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:15.891][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-06 19:59:15.891][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-06 19:59:15.892][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:15.892][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-06 19:59:15.893][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:15.893][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:15.893][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-06 19:59:15.894][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:15.894][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-06 19:59:15.895][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-06 19:59:15.895][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:15.895][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-06 19:59:15.896][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-06 19:59:15.896][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-06 19:59:15.896][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-06 19:59:15.897][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-06 19:59:15.897][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-06 19:59:15.897][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-06 19:59:15.898][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-06 19:59:15.898][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-06 19:59:15.899][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-06 19:59:15.899][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-06 19:59:15.899][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-06 19:59:15.900][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-06 19:59:15.900][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-06 19:59:15.900][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-06 19:59:15.901][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-06 19:59:15.901][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-06 19:59:15.901][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-06 19:59:15.902][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-06 19:59:15.902][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-06 19:59:15.903][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-06 19:59:15.903][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-06 19:59:15.903][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-06 19:59:15.904][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-06 19:59:15.904][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-06 19:59:15.904][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-06 19:59:15.905][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-06 19:59:15.905][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-06 19:59:15.905][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-06 19:59:15.906][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-06 19:59:15.906][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-06 19:59:15.907][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-06 19:59:15.907][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-06 19:59:15.907][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-06 19:59:15.908][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-06 19:59:15.908][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-06 19:59:15.908][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-06 19:59:15.909][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-06 19:59:15.909][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-06 19:59:15.909][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-06 19:59:15.910][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-06 19:59:15.910][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-06 19:59:15.911][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-06 19:59:15.911][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-06 19:59:15.911][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-06 19:59:15.912][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-06 19:59:15.912][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-06 19:59:15.912][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:15.913][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:15.913][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-06 19:59:15.914][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-06 19:59:15.914][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-06 19:59:15.914][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-06 19:59:15.915][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-06 19:59:15.915][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-06 19:59:15.915][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-06 19:59:15.916][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-06 19:59:15.916][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-06 19:59:15.916][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-06 19:59:15.917][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-06 19:59:15.917][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-06 19:59:15.918][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-06 19:59:15.918][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-06 19:59:15.918][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-06 19:59:15.919][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-06 19:59:15.919][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:15.920][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:15.920][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.920][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.930][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[2024-05-06 19:59:15.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.931][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[2024-05-06 19:59:15.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:15.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:15.948][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:15.948][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.949][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.949][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.950][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:15.950][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.951][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.951][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-06 19:59:15.951][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-06 19:59:15.951][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:15.952][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.952][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-06 19:59:15.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:15.953][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-06 19:59:15.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.954][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:15.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:15.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:15.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:15.955][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-06 19:59:15.955][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-06 19:59:15.955][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:15.956][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:15.956][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:15.956][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-06 19:59:15.956][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-06 19:59:15.956][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:15.957][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:15.957][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-06 19:59:15.958][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:15.958][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:15.959][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:15.960][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.960][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-06 19:59:15.960][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-06 19:59:15.961][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-06 19:59:15.961][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-06 19:59:15.961][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-06 19:59:15.962][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-06 19:59:15.962][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-06 19:59:15.965][biodb::testThat]
biodb.INFO [2024-05-06 19:59:15.965][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-05-06 19:59:15.965][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:15.966][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:15.967][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-06 19:59:15.968][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.968][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-06 19:59:15.969][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.969][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-06 19:59:15.970][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-06 19:59:15.971][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:15.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-06 19:59:15.972][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.972][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-05-06 19:59:15.973][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-05-06 19:59:15.974][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-06 19:59:15.974][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-05-06 19:59:15.975][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:15.976][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2024-05-06 19:59:15.977][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:15.977][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-06 19:59:15.977][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-06 19:59:15.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:15.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:15.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:15.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:15.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:15.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:15.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:15.983][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.983][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:15.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:15.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.985][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:15.985][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:15.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.986][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.986][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-06 19:59:15.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-06 19:59:15.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.987][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:15.987][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:15.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.988][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:15.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:15.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.989][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-06 19:59:15.990][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-06 19:59:15.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.990][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.990][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.991][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-06 19:59:15.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.991][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.992][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.992][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.992][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.993][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:15.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.994][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:15.994][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:15.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.995][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.995][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-06 19:59:15.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:15.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.996][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.996][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.997][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:15.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.998][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:15.998][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:15.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:15.999][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:15.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:16.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:16.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.001][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:16.001][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:16.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.002][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-06 19:59:16.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-06 19:59:16.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.003][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:16.003][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:16.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.003][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.004][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-06 19:59:16.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-06 19:59:16.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:16.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:16.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:16.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:16.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:16.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:16.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:16.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:16.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:16.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:16.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:16.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:16.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:16.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:16.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:16.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:16.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:16.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:16.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:16.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:16.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:16.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:16.015][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-05-06 19:59:16.016][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-06 19:59:16.017][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-06 19:59:16.017][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-06 19:59:16.018][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-06 19:59:16.018][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:16.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:16.018][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:16.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:16.019][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:16.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 129 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_100_generic.R:16:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
── Failure ('test_100_generic.R:16:1'): We can search for an entry by name. ────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for an entry by name. ──────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
── Failure ('test_100_generic.R:16:1'): We can load an entry from the database. ──
any(vapply(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 = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_100_generic.R:16:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for a compound ─────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
── Error ('test_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── 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 = `<ChebiCnn>`, 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 = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)

[ FAIL 14 | WARN 0 | SKIP 0 | PASS 129 ]
Error: Test failures
Execution halted

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn0.7620.2342.374
ChebiEntry0.1200.0050.126