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This page was generated on 2025-06-10 12:09 -0400 (Tue, 10 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4794
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4573
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4512
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4480
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.15.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-06-09 13:25 -0400 (Mon, 09 Jun 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: 1a7ef22
git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

CHECK results for biodbChebi on kjohnson3

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

raw results


Summary

Package: biodbChebi
Version: 1.15.0
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_1.15.0.tar.gz
StartedAt: 2025-06-09 18:14:29 -0400 (Mon, 09 Jun 2025)
EndedAt: 2025-06-09 18:15:15 -0400 (Mon, 09 Jun 2025)
EllapsedTime: 45.6 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.15.0’
* 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-3.22-bioc/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/4.5-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.15.0’
** 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 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 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 [2025-06-09 18:14:48.267][biodb::testContext]
biodb.INFO [2025-06-09 18:14:48.269][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-09 18:14:48.269][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-06-09 18:14:48.269][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-09 18:14:48.270][biodb::testContext]
biodb.INFO [2025-06-09 18:14:48.272][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.0.
biodb.DEBUG[2025-06-09 18:14:48.273][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-06-09 18:14:48.276][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:14:48.276][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-09 18:14:48.277][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-09 18:14:48.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.278][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-09 18:14:48.284][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-09 18:14:48.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.285][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-09 18:14:48.285][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-09 18:14:48.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.286][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-09 18:14:48.287][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-09 18:14:48.287][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-09 18:14:48.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.288][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-09 18:14:48.288][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-09 18:14:48.288][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-09 18:14:48.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.289][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-09 18:14:48.290][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-09 18:14:48.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.290][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-09 18:14:48.291][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-09 18:14:48.291][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-09 18:14:48.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.292][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-09 18:14:48.292][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-09 18:14:48.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.293][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-09 18:14:48.293][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-09 18:14:48.294][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-09 18:14:48.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.295][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-09 18:14:48.295][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-09 18:14:48.295][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-09 18:14:48.295][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-09 18:14:48.296][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-09 18:14:48.296][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-09 18:14:48.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.297][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-09 18:14:48.297][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-09 18:14:48.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.298][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-09 18:14:48.298][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-09 18:14:48.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.299][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-09 18:14:48.299][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-09 18:14:48.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.300][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-09 18:14:48.300][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-06-09 18:14:48.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.301][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-09 18:14:48.302][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-09 18:14:48.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.303][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-09 18:14:48.303][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-09 18:14:48.309][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-09 18:14:48.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.310][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-09 18:14:48.310][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-09 18:14:48.310][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-09 18:14:48.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.313][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-09 18:14:48.324][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.332][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-06-09 18:14:48.333][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.333][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:14:48.333][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.333][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.334][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.334][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.334][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-09 18:14:48.335][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:14:48.335][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.335][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-09 18:14:48.335][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:14:48.336][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.336][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.336][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:14:48.336][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:14:48.336][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:14:48.336][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-09 18:14:48.336][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-09 18:14:48.336][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:14:48.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.337][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:14:48.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.338][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.338][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.338][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:14:48.339][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:14:48.339][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.339][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.339][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-09 18:14:48.340][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.340][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-09 18:14:48.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.341][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:14:48.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.341][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.342][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.342][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.342][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-09 18:14:48.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:14:48.343][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.343][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-09 18:14:48.343][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:14:48.343][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.344][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.344][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:14:48.344][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:14:48.344][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:14:48.344][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-09 18:14:48.344][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-09 18:14:48.344][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:14:48.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.345][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:14:48.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.346][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.346][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.346][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:14:48.346][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:14:48.347][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.347][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.347][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-09 18:14:48.348][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.348][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-06-09 18:14:48.348][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.348][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:14:48.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.349][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.349][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.349][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.350][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-09 18:14:48.350][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:14:48.350][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.350][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-09 18:14:48.351][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:14:48.351][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.351][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.351][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.352][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:14:48.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.352][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:14:48.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.353][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.353][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.353][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:14:48.354][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:14:48.354][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.354][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.355][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-09 18:14:48.355][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.355][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-09 18:14:48.356][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.356][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:14:48.356][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.356][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.357][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.357][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.357][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-09 18:14:48.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:14:48.358][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.358][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-09 18:14:48.358][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:14:48.358][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.359][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.359][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.359][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:14:48.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.360][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:14:48.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.361][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.361][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:14:48.361][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:14:48.361][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.362][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:14:48.363][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:14:48.363][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.368][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[2025-06-09 18:14:48.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.369][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[2025-06-09 18:14:48.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.371][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[2025-06-09 18:14:48.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.373][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[2025-06-09 18:14:48.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.374][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[2025-06-09 18:14:48.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.376][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[2025-06-09 18:14:48.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.380][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[2025-06-09 18:14:48.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.382][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[2025-06-09 18:14:48.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.383][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[2025-06-09 18:14:48.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.384][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[2025-06-09 18:14:48.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.385][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[2025-06-09 18:14:48.385][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-09 18:14:48.387][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-09 18:14:48.388][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-09 18:14:48.388][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-09 18:14:48.388][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-09 18:14:48.389][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-09 18:14:48.389][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-09 18:14:48.390][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-09 18:14:48.390][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-09 18:14:48.390][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-09 18:14:48.391][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-09 18:14:48.391][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-09 18:14:48.391][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-09 18:14:48.392][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-09 18:14:48.392][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-09 18:14:48.392][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-09 18:14:48.393][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-09 18:14:48.393][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-09 18:14:48.394][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-09 18:14:48.394][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-09 18:14:48.394][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-09 18:14:48.395][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-09 18:14:48.395][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-09 18:14:48.395][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-09 18:14:48.396][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-09 18:14:48.396][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-09 18:14:48.397][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-09 18:14:48.397][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-09 18:14:48.397][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-09 18:14:48.398][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-09 18:14:48.398][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-09 18:14:48.398][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-09 18:14:48.399][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-09 18:14:48.399][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-09 18:14:48.399][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-09 18:14:48.400][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-09 18:14:48.400][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-09 18:14:48.401][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-09 18:14:48.401][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-09 18:14:48.401][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-09 18:14:48.402][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-09 18:14:48.402][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-09 18:14:48.402][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-09 18:14:48.403][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-09 18:14:48.403][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-09 18:14:48.403][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-09 18:14:48.404][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-09 18:14:48.404][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-09 18:14:48.405][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-09 18:14:48.405][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-09 18:14:48.405][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-09 18:14:48.406][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-09 18:14:48.406][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-09 18:14:48.406][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-09 18:14:48.407][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-09 18:14:48.407][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-09 18:14:48.407][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-09 18:14:48.408][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-09 18:14:48.408][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-09 18:14:48.409][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-09 18:14:48.409][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-09 18:14:48.409][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-09 18:14:48.410][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-09 18:14:48.410][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-09 18:14:48.410][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-09 18:14:48.411][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-09 18:14:48.411][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-09 18:14:48.411][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-09 18:14:48.412][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-09 18:14:48.412][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-09 18:14:48.413][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-09 18:14:48.413][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-09 18:14:48.413][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-09 18:14:48.414][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-09 18:14:48.414][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-09 18:14:48.414][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-09 18:14:48.415][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-09 18:14:48.415][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-09 18:14:48.415][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-09 18:14:48.416][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-09 18:14:48.416][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-09 18:14:48.417][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-09 18:14:48.417][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-09 18:14:48.419][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-09 18:14:48.419][initialize] This is biodb version 1.17.0.
biodb.DEBUG[2025-06-09 18:14:48.421][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:14:48.421][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.421][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.422][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[2025-06-09 18:14:48.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.424][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[2025-06-09 18:14:48.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.426][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[2025-06-09 18:14:48.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.430][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[2025-06-09 18:14:48.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.432][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[2025-06-09 18:14:48.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.433][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[2025-06-09 18:14:48.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.435][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[2025-06-09 18:14:48.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.436][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[2025-06-09 18:14:48.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.438][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[2025-06-09 18:14:48.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.440][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[2025-06-09 18:14:48.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.441][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[2025-06-09 18:14:48.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.444][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[2025-06-09 18:14:48.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.446][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[2025-06-09 18:14:48.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.447][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[2025-06-09 18:14:48.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:14:48.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:14:48.453][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-06-09 18:14:48.456][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-06-09 18:14:48.456][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.457][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.457][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.457][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:14:48.458][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.458][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.458][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.458][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-06-09 18:14:48.459][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-09 18:14:48.459][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:14:48.459][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.459][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:14:48.460][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:14:48.461][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-09 18:14:48.461][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:14:48.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:14:48.462][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:14:48.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:14:48.462][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-06-09 18:14:48.462][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-06-09 18:14:48.463][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:14:48.463][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:14:48.463][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-09 18:14:48.463][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-06-09 18:14:48.463][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-06-09 18:14:48.465][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-09 18:14:48.466][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-09 18:14:48.466][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-06-09 18:14:48.467][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-09 18:14:48.467][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-09 18:14:48.467][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-09 18:14:48.478][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-06-09 18:14:48.478][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-06-09 18:14:48.480][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-06-09 18:14:48.481][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-06-09 18:14:48.483][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-06-09 18:14:48.483][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-06-09 18:14:48.484][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-06-09 18:14:48.484][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-06-09 18:14:48.499][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.500][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-06-09 18:14:48.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:14:48.500][biodb::testThat]
biodb.TRACE[2025-06-09 18:14:48.502][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-06-09 18:14:48.503][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-06-09 18:14:48.504][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-06-09 18:14:48.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:14:48.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-09 18:14:48.518][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.519][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.525][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.525][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.526][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.534][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.536][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.536][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.536][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.538][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.538][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.539][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.540][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.540][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.541][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.542][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.542][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.543][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.543][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.544][ef$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:14:48.545][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.545][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.545][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:14:48.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.547][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.547][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.547][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.549][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.549][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.549][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.551][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:14:48.551][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.552][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.556][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:14:48.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.557][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.558][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.558][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.559][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-09 18:14:48.582][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-06-09 18:14:48.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-09 18:14:48.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-09 18:14:48.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.600][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-09 18:14:48.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-09 18:14:48.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.601][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-09 18:14:48.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-09 18:14:48.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.602][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-09 18:14:48.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-09 18:14:48.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.636][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.636][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.637][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.644][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.644][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.645][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.655][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.656][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.660][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.661][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.662][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.663][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.663][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.664][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.664][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.671][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.671][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.672][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.679][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.679][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.680][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.684][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.685][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.686][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.687][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.687][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.688][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.688][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.692][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.696][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.697][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.698][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.698][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.699][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.699][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.703][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.704][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.705][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.706][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.706][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.707][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.707][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.712][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.713][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.714][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.714][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.715][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.715][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.722][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.722][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.723][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.730][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.730][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.731][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.735][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.735][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.736][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.737][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.738][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.738][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.742][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.743][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.745][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.745][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.746][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.747][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.748][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.748][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.750][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.750][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.751][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.753][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.753][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.753][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.755][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.755][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.756][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.758][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.758][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.758][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.760][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.761][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.762][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.763][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.763][ef$get] fields variable is a list.
biodb.INFO [2025-06-09 18:14:48.766][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.766][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-06-09 18:14:48.767][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:14:48.767][biodb::testThat]
biodb.DEBUG[2025-06-09 18:14:48.772][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-06-09 18:14:48.775][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-06-09 18:14:48.776][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-06-09 18:14:48.776][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:14:48.777][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-06-09 18:14:48.777][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-06-09 18:14:48.785][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-06-09 18:14:48.785][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-06-09 18:14:48.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:14:48.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:14:48.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:14:48.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:14:48.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:14:48.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:14:48.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-09 18:14:48.790][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.793][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.794][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.801][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:14:48.801][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:14:48.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.802][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.803][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:14:48.803][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:14:48.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.804][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.804][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:14:48.804][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:14:48.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.805][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.805][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.805][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:14:48.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.806][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.806][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.807][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:14:48.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.807][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.808][ef$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:14:48.808][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:14:48.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.808][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.809][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.809][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:14:48.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.810][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.810][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.810][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.811][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.811][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:14:48.811][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:14:48.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.812][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.812][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:14:48.812][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:14:48.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.813][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:14:48.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:14:48.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:14:48.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:14:48.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-09 18:14:48.824][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-06-09 18:14:48.824][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-06-09 18:14:48.831][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.831][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-06-09 18:14:48.831][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:14:48.831][biodb::testThat]
biodb.TRACE[2025-06-09 18:14:48.832][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:14:48.833][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:14:48.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:14:48.833][ef$get] fields variable is a list.
biodb.DEBUG[2025-06-09 18:14:48.834][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.INFO [2025-06-09 18:14:48.903][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.904][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-06-09 18:14:48.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:14:48.904][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.917][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.918][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-06-09 18:14:48.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:14:48.918][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.936][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.937][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-06-09 18:14:48.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:14:48.937][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.940][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.940][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-06-09 18:14:48.940][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:14:48.941][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.943][biodb::testThat]
biodb.INFO [2025-06-09 18:14:48.944][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-06-09 18:14:48.944][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:14:48.944][biodb::testThat]
biodb.DEBUG[2025-06-09 18:14:48.945][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-06-09 18:14:59.388][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-06-09 18:15:09.940][biodb::testThat]
biodb.INFO [2025-06-09 18:15:09.940][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-06-09 18:15:09.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:09.941][biodb::testThat]
biodb.DEBUG[2025-06-09 18:15:10.270][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[2025-06-09 18:15:10.618][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:10.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:10.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.619][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.619][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.620][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.620][ef$get] fields variable is a list.
biodb.INFO [2025-06-09 18:15:10.621][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.621][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-06-09 18:15:10.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.622][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.633][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.634][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-06-09 18:15:10.634][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.634][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.713][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.714][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-06-09 18:15:10.714][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.714][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.719][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.719][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-06-09 18:15:10.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.719][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.724][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.724][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-06-09 18:15:10.724][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.724][biodb::testThat]
biodb.DEBUG[2025-06-09 18:15:10.725][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-06-09 18:15:10.739][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-06-09 18:15:10.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-06-09 18:15:10.746][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:10.746][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2025-06-09 18:15:10.747][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-06-09 18:15:10.747][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-06-09 18:15:10.747][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-06-09 18:15:10.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:10.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:10.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:10.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:10.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:10.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:10.751][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.TRACE[2025-06-09 18:15:10.752][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.753][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.754][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:15:10.754][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:15:10.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.755][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.755][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:15:10.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:15:10.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.756][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.756][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:15:10.757][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:15:10.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.757][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.757][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.758][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.758][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.758][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.759][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.759][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.760][ef$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:15:10.760][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:15:10.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.760][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.761][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.761][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.762][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:10.762][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:10.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.763][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.763][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:15:10.763][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:15:10.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.764][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.764][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:15:10.764][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:15:10.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.765][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-09 18:15:10.776][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-06-09 18:15:10.776][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-06-09 18:15:10.782][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.782][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-06-09 18:15:10.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.783][biodb::testThat]
biodb.DEBUG[2025-06-09 18:15:10.787][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-06-09 18:15:10.787][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-06-09 18:15:10.788][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-06-09 18:15:10.788][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-06-09 18:15:10.789][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2025-06-09 18:15:10.790][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[2025-06-09 18:15:10.790][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-06-09 18:15:10.791][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-06-09 18:15:10.791][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-06-09 18:15:10.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:10.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:10.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:10.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:10.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:10.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:10.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-09 18:15:10.796][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.796][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.797][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.799][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:15:10.799][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:15:10.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.800][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.800][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:15:10.800][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:15:10.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.801][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.801][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:15:10.802][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:15:10.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.802][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.803][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.803][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.803][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.804][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.804][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.805][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.805][ef$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:15:10.805][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:15:10.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.806][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.806][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.807][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.807][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.807][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:10.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:10.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.808][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.809][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:15:10.809][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:15:10.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.810][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.810][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:15:10.810][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:15:10.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.811][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-09 18:15:10.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:10.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:10.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:10.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:10.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:10.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:10.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-09 18:15:10.827][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.828][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.828][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.830][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:15:10.830][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:15:10.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.831][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.831][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:15:10.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:15:10.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.832][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:15:10.832][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:15:10.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.833][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.833][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:15:10.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:15:10.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.834][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:15:10.835][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:15:10.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.835][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:15:10.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:15:10.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.836][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.837][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.837][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.839][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.839][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.840][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.840][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.841][ef$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:15:10.841][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:15:10.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.842][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.842][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:15:10.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:15:10.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.843][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.844][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.844][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.846][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:10.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:10.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.846][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:10.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:10.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.848][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:15:10.848][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:15:10.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.848][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.849][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:15:10.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:15:10.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.850][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:15:10.850][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:15:10.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.850][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.851][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:15:10.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:15:10.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-09 18:15:10.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:10.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:10.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:10.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:10.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:10.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:10.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-09 18:15:10.863][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.863][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.864][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.865][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:15:10.865][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:15:10.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.866][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.866][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:15:10.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:15:10.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.867][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:15:10.867][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:15:10.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.868][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.868][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:15:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:15:10.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.869][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:15:10.870][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:15:10.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.870][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:15:10.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:15:10.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.871][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.872][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.872][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:15:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.873][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.874][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.874][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.874][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:10.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.875][ef$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:15:10.876][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:15:10.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.876][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.876][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:15:10.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:15:10.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.877][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.878][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.878][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.879][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:10.880][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:10.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.880][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:10.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:10.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.882][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:15:10.882][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:15:10.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.882][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.883][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:15:10.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:15:10.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.884][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:15:10.884][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:15:10.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.884][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.885][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:15:10.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:15:10.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:10.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:10.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:10.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-09 18:15:10.902][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-06-09 18:15:10.902][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-06-09 18:15:10.902][function(conn, opt)] Entries: [4]: "NULL, NULL, <environment>, <environment>"
biodb.INFO [2025-06-09 18:15:10.911][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.912][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-06-09 18:15:10.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.912][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.924][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.924][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-06-09 18:15:10.925][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.925][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.927][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.928][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-06-09 18:15:10.928][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.928][biodb::testThat]
biodb.DEBUG[2025-06-09 18:15:10.930][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-06-09 18:15:10.938][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:10.939][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-06-09 18:15:10.939][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:10.940][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-06-09 18:15:10.947][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:10.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:10.948][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2025-06-09 18:15:10.949][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:10.949][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2025-06-09 18:15:10.953][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:10.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:10.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.954][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:10.954][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.955][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:10.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:10.955][ef$get] fields variable is a list.
biodb.INFO [2025-06-09 18:15:10.956][biodb::testThat]
biodb.INFO [2025-06-09 18:15:10.956][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-06-09 18:15:10.956][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:10.956][biodb::testThat]
biodb.ERROR[2025-06-09 18:15:10.977][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-06-09 18:15:10.982][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-06-09 18:15:10.985][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-06-09 18:15:10.986][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-06-09 18:15:10.986][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-06-09 18:15:10.986][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-09 18:15:10.987][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:10.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:10.987][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:10.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:10.988][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:10.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-06-09 18:15:10.991][biodb::testContext]
biodb.INFO [2025-06-09 18:15:10.991][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-09 18:15:10.992][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-06-09 18:15:10.992][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-09 18:15:10.992][biodb::testContext]
biodb.INFO [2025-06-09 18:15:10.993][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.0.
biodb.DEBUG[2025-06-09 18:15:10.993][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-06-09 18:15:10.995][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:10.995][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-09 18:15:10.995][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-09 18:15:10.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:10.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:10.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:10.996][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-09 18:15:10.997][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-09 18:15:10.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:10.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:10.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:10.997][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-09 18:15:10.998][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-09 18:15:10.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:10.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:10.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:10.999][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-09 18:15:10.999][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-09 18:15:10.999][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-09 18:15:10.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.000][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-09 18:15:11.000][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-09 18:15:11.001][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.002][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-09 18:15:11.002][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-09 18:15:11.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.003][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-09 18:15:11.003][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-09 18:15:11.003][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-09 18:15:11.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.004][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-09 18:15:11.004][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.005][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-09 18:15:11.006][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-09 18:15:11.006][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.007][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-09 18:15:11.007][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-09 18:15:11.007][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-09 18:15:11.007][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-09 18:15:11.008][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-09 18:15:11.008][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-09 18:15:11.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.009][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-09 18:15:11.009][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-09 18:15:11.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.010][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-09 18:15:11.010][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-09 18:15:11.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.011][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-09 18:15:11.011][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-09 18:15:11.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.012][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-09 18:15:11.013][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-06-09 18:15:11.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.014][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-09 18:15:11.014][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-09 18:15:11.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.015][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-09 18:15:11.015][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-09 18:15:11.021][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-09 18:15:11.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.022][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-09 18:15:11.022][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-09 18:15:11.022][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-09 18:15:11.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.023][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-09 18:15:11.024][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.024][self$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[2025-06-09 18:15:11.024][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.025][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.025][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.026][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-09 18:15:11.026][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.026][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.027][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-09 18:15:11.027][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.027][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.027][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.028][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.028][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.028][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.028][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-09 18:15:11.028][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-09 18:15:11.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.029][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.030][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.030][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.030][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.030][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.030][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.031][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-09 18:15:11.031][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.032][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-09 18:15:11.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.032][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.032][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.033][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.033][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.033][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-09 18:15:11.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.034][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.034][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-09 18:15:11.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.035][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.035][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.035][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.035][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.035][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-09 18:15:11.035][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-09 18:15:11.035][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.036][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.037][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.037][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.038][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.038][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.038][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-09 18:15:11.039][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.039][self$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[2025-06-09 18:15:11.039][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.040][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.040][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.040][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.040][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.041][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.041][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-09 18:15:11.041][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.041][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.042][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-09 18:15:11.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.042][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.042][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.043][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.043][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.044][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.047][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.047][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.048][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.048][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.048][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.048][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.049][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-09 18:15:11.049][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.049][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-09 18:15:11.050][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.050][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.050][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.051][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.051][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.051][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-09 18:15:11.052][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.052][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.052][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-09 18:15:11.052][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.053][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.053][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.053][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.053][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.054][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.055][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.055][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.055][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.056][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.056][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.056][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:11.056][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.076][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-09 18:15:11.076][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-09 18:15:11.077][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-09 18:15:11.077][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-09 18:15:11.077][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-09 18:15:11.078][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-09 18:15:11.078][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-09 18:15:11.078][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-09 18:15:11.079][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-09 18:15:11.079][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-09 18:15:11.080][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-09 18:15:11.080][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-09 18:15:11.080][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-09 18:15:11.081][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-09 18:15:11.081][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-09 18:15:11.081][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-09 18:15:11.082][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-09 18:15:11.082][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-09 18:15:11.082][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-09 18:15:11.083][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-09 18:15:11.083][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-09 18:15:11.084][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-09 18:15:11.084][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-09 18:15:11.084][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-09 18:15:11.085][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-09 18:15:11.085][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-09 18:15:11.085][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-09 18:15:11.086][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-09 18:15:11.086][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-09 18:15:11.086][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-09 18:15:11.087][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-09 18:15:11.087][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-09 18:15:11.088][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-09 18:15:11.088][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-09 18:15:11.088][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-09 18:15:11.089][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-09 18:15:11.089][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-09 18:15:11.089][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-09 18:15:11.090][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-09 18:15:11.090][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-09 18:15:11.090][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-09 18:15:11.091][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-09 18:15:11.091][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-09 18:15:11.092][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-09 18:15:11.092][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-09 18:15:11.092][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-09 18:15:11.093][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-09 18:15:11.093][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-09 18:15:11.093][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-09 18:15:11.094][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-09 18:15:11.094][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-09 18:15:11.094][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-09 18:15:11.095][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-09 18:15:11.095][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-09 18:15:11.095][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-09 18:15:11.096][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-09 18:15:11.096][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-09 18:15:11.097][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-09 18:15:11.097][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-09 18:15:11.097][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-09 18:15:11.098][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-09 18:15:11.098][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-09 18:15:11.098][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-09 18:15:11.099][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-09 18:15:11.099][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-09 18:15:11.099][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-09 18:15:11.100][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-09 18:15:11.100][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-09 18:15:11.101][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-09 18:15:11.101][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-09 18:15:11.101][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-09 18:15:11.102][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-09 18:15:11.102][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-09 18:15:11.102][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-09 18:15:11.103][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-09 18:15:11.103][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-09 18:15:11.103][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-09 18:15:11.104][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-09 18:15:11.104][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-09 18:15:11.104][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-09 18:15:11.105][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-09 18:15:11.105][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-09 18:15:11.106][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-09 18:15:11.107][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-09 18:15:11.108][initialize] This is biodb version 1.17.0.
biodb.DEBUG[2025-06-09 18:15:11.108][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:11.109][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.109][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.114][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.DEBUG[2025-06-09 18:15:11.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.136][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-06-09 18:15:11.137][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.137][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.138][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.138][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.138][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.138][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.139][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.139][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.139][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-06-09 18:15:11.139][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-09 18:15:11.140][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.140][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.140][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.141][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.142][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-09 18:15:11.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.142][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.143][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.143][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-06-09 18:15:11.143][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-06-09 18:15:11.144][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.146][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.146][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.147][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-06-09 18:15:11.147][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-06-09 18:15:11.147][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-09 18:15:11.147][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-09 18:15:11.148][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-06-09 18:15:11.148][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-09 18:15:11.149][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-09 18:15:11.149][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-09 18:15:11.150][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.150][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-06-09 18:15:11.151][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.151][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-06-09 18:15:11.151][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-06-09 18:15:11.152][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-06-09 18:15:11.152][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-06-09 18:15:11.152][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-06-09 18:15:11.153][biodb::testThat]
biodb.INFO [2025-06-09 18:15:11.153][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-06-09 18:15:11.153][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:11.153][biodb::testThat]
biodb.DEBUG[2025-06-09 18:15:11.154][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-06-09 18:15:11.156][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.156][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-06-09 18:15:11.156][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.158][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-06-09 18:15:11.160][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.161][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.161][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-06-09 18:15:11.161][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.162][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-06-09 18:15:11.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.170][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.171][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-06-09 18:15:11.172][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.173][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-06-09 18:15:11.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.185][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.DEBUG[2025-06-09 18:15:11.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.187][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-06-09 18:15:11.188][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.188][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-06-09 18:15:11.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.192][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.193][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.193][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-06-09 18:15:11.194][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.194][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-06-09 18:15:11.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.201][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.202][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.203][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-06-09 18:15:11.203][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.203][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-06-09 18:15:11.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.207][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.208][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.209][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-06-09 18:15:11.209][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.209][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-06-09 18:15:11.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.213][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.214][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.215][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-06-09 18:15:11.215][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.216][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-06-09 18:15:11.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-06-09 18:15:11.221][biodb::testThat]
biodb.INFO [2025-06-09 18:15:11.221][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-06-09 18:15:11.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:11.222][biodb::testThat]
biodb.DEBUG[2025-06-09 18:15:11.223][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.224][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2025-06-09 18:15:11.225][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.225][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2025-06-09 18:15:11.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.230][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.231][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.232][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2025-06-09 18:15:11.232][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.232][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2025-06-09 18:15:11.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-06-09 18:15:11.237][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-06-09 18:15:11.237][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-06-09 18:15:11.238][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-06-09 18:15:11.238][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-09 18:15:11.238][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.239][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.239][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-06-09 18:15:11.241][biodb::testContext]
biodb.INFO [2025-06-09 18:15:11.241][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-09 18:15:11.241][biodb::testContext] Test context - Test web services
biodb.INFO [2025-06-09 18:15:11.241][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-09 18:15:11.242][biodb::testContext]
biodb.INFO [2025-06-09 18:15:11.242][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.0.
biodb.DEBUG[2025-06-09 18:15:11.243][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-06-09 18:15:11.244][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:11.245][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-09 18:15:11.245][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.246][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-09 18:15:11.246][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.247][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-09 18:15:11.247][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.248][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-09 18:15:11.248][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-09 18:15:11.249][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-09 18:15:11.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.250][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-09 18:15:11.250][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-09 18:15:11.250][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.251][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-09 18:15:11.251][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-09 18:15:11.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.252][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-09 18:15:11.252][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-09 18:15:11.253][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-09 18:15:11.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.254][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-09 18:15:11.254][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.255][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-09 18:15:11.255][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-09 18:15:11.255][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.256][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-09 18:15:11.256][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-09 18:15:11.257][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-09 18:15:11.257][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-09 18:15:11.257][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-09 18:15:11.257][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-09 18:15:11.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.258][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-09 18:15:11.259][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-09 18:15:11.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.260][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-09 18:15:11.260][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-09 18:15:11.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.261][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-09 18:15:11.261][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-09 18:15:11.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.262][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-09 18:15:11.262][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-06-09 18:15:11.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.263][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-09 18:15:11.263][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-09 18:15:11.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.264][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-09 18:15:11.264][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-09 18:15:11.273][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-09 18:15:11.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.274][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-09 18:15:11.274][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-09 18:15:11.274][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-09 18:15:11.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.275][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-09 18:15:11.276][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.276][self$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[2025-06-09 18:15:11.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.277][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.277][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.277][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.277][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.277][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.278][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-09 18:15:11.278][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.278][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.278][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-09 18:15:11.279][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.279][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.279][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.279][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.279][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.279][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.279][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-09 18:15:11.279][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-09 18:15:11.280][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.280][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.281][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.281][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.282][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.282][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.282][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.282][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.283][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-09 18:15:11.283][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.283][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-09 18:15:11.284][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.284][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.284][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.284][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.285][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.285][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.285][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-09 18:15:11.285][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.286][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.286][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-09 18:15:11.286][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.286][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.287][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.287][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.287][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.287][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.287][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-09 18:15:11.287][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-09 18:15:11.287][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.287][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.288][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.288][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.289][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.289][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.289][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.289][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.289][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.290][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.290][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-09 18:15:11.290][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.291][self$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[2025-06-09 18:15:11.291][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.291][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.291][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.292][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.292][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.292][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-09 18:15:11.293][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.293][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.293][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-09 18:15:11.293][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.294][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.294][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.294][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.294][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.295][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.295][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.296][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.296][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.296][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.297][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.297][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.297][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-09 18:15:11.298][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.298][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-09 18:15:11.298][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.299][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.299][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.299][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.300][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.300][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-09 18:15:11.300][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.300][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.301][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-09 18:15:11.301][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.301][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.301][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.302][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.302][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.303][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.303][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.303][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.304][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.304][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.304][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.305][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:11.305][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.323][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[2025-06-09 18:15:11.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.324][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-09 18:15:11.325][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-09 18:15:11.325][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-09 18:15:11.325][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-09 18:15:11.326][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-09 18:15:11.326][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-09 18:15:11.327][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-09 18:15:11.327][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-09 18:15:11.327][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-09 18:15:11.328][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-09 18:15:11.328][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-09 18:15:11.328][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-09 18:15:11.329][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-09 18:15:11.329][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-09 18:15:11.330][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-09 18:15:11.330][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-09 18:15:11.330][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-09 18:15:11.331][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-09 18:15:11.331][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-09 18:15:11.331][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-09 18:15:11.332][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-09 18:15:11.332][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-09 18:15:11.332][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-09 18:15:11.333][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-09 18:15:11.333][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-09 18:15:11.334][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-09 18:15:11.334][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-09 18:15:11.334][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-09 18:15:11.335][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-09 18:15:11.335][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-09 18:15:11.335][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-09 18:15:11.336][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-09 18:15:11.336][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-09 18:15:11.336][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-09 18:15:11.337][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-09 18:15:11.337][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-09 18:15:11.338][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-09 18:15:11.338][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-09 18:15:11.338][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-09 18:15:11.339][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-09 18:15:11.339][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-09 18:15:11.339][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-09 18:15:11.340][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-09 18:15:11.340][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-09 18:15:11.340][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-09 18:15:11.341][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-09 18:15:11.341][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-09 18:15:11.342][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-09 18:15:11.342][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-09 18:15:11.342][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-09 18:15:11.343][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-09 18:15:11.343][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-09 18:15:11.343][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-09 18:15:11.344][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-09 18:15:11.344][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-09 18:15:11.344][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-09 18:15:11.345][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-09 18:15:11.345][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-09 18:15:11.345][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-09 18:15:11.346][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-09 18:15:11.346][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-09 18:15:11.347][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-09 18:15:11.347][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-09 18:15:11.347][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-09 18:15:11.348][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-09 18:15:11.348][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-09 18:15:11.348][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-09 18:15:11.349][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-09 18:15:11.349][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-09 18:15:11.350][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-09 18:15:11.350][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-09 18:15:11.350][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-09 18:15:11.351][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-09 18:15:11.351][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-09 18:15:11.351][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-09 18:15:11.352][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-09 18:15:11.352][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-09 18:15:11.352][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-09 18:15:11.353][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-09 18:15:11.353][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-09 18:15:11.353][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-09 18:15:11.354][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-09 18:15:11.354][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-09 18:15:11.355][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-09 18:15:11.355][initialize] This is biodb version 1.17.0.
biodb.DEBUG[2025-06-09 18:15:11.355][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:11.356][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.356][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.361][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[2025-06-09 18:15:11.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.373][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[2025-06-09 18:15:11.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.376][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[2025-06-09 18:15:11.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.378][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[2025-06-09 18:15:11.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.382][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[2025-06-09 18:15:11.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.384][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[2025-06-09 18:15:11.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.385][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[2025-06-09 18:15:11.386][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-06-09 18:15:11.386][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.387][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.387][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.388][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.388][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.388][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.389][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.389][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-06-09 18:15:11.389][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-09 18:15:11.389][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-06-09 18:15:11.390][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-06-09 18:15:11.391][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.391][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.391][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.391][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.391][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-09 18:15:11.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.392][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.393][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-06-09 18:15:11.393][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-06-09 18:15:11.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.394][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.394][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-06-09 18:15:11.394][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-06-09 18:15:11.394][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-09 18:15:11.395][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-09 18:15:11.395][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-06-09 18:15:11.396][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-09 18:15:11.396][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-09 18:15:11.396][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-09 18:15:11.397][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.398][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-06-09 18:15:11.398][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.398][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-06-09 18:15:11.399][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-06-09 18:15:11.399][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-06-09 18:15:11.399][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-06-09 18:15:11.400][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-06-09 18:15:11.400][biodb::testThat]
biodb.INFO [2025-06-09 18:15:11.400][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-06-09 18:15:11.401][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:11.401][biodb::testThat]
biodb.DEBUG[2025-06-09 18:15:11.402][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-06-09 18:15:11.403][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.403][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-06-09 18:15:11.404][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.404][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-06-09 18:15:11.405][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.407][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-06-09 18:15:11.407][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.408][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2025-06-09 18:15:11.411][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-06-09 18:15:11.411][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-06-09 18:15:11.411][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-06-09 18:15:11.412][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-09 18:15:11.412][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.412][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.413][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-06-09 18:15:11.414][biodb::testContext]
biodb.INFO [2025-06-09 18:15:11.415][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-09 18:15:11.415][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-06-09 18:15:11.415][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-09 18:15:11.416][biodb::testContext]
biodb.INFO [2025-06-09 18:15:11.416][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.0.
biodb.DEBUG[2025-06-09 18:15:11.417][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-06-09 18:15:11.418][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:11.419][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-09 18:15:11.419][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.420][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[2025-06-09 18:15:11.420][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-09 18:15:11.420][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.421][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-09 18:15:11.422][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.422][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[2025-06-09 18:15:11.423][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-09 18:15:11.423][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-09 18:15:11.423][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-09 18:15:11.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.424][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-09 18:15:11.424][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-09 18:15:11.425][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.425][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-09 18:15:11.426][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-09 18:15:11.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.427][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-09 18:15:11.427][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-09 18:15:11.427][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-09 18:15:11.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.428][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[2025-06-09 18:15:11.428][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-09 18:15:11.428][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.429][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-09 18:15:11.429][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-09 18:15:11.430][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-09 18:15:11.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.430][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[2025-06-09 18:15:11.431][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-09 18:15:11.431][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-09 18:15:11.431][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-09 18:15:11.431][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-09 18:15:11.432][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-09 18:15:11.432][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-09 18:15:11.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.433][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-09 18:15:11.433][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-09 18:15:11.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.434][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[2025-06-09 18:15:11.434][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-09 18:15:11.434][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-09 18:15:11.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.435][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-09 18:15:11.435][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-09 18:15:11.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.436][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[2025-06-09 18:15:11.436][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-09 18:15:11.436][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-06-09 18:15:11.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.437][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-09 18:15:11.438][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-09 18:15:11.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.438][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[2025-06-09 18:15:11.439][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-09 18:15:11.439][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-09 18:15:11.443][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-09 18:15:11.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.444][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-09 18:15:11.445][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-09 18:15:11.445][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-09 18:15:11.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.446][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[2025-06-09 18:15:11.446][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-09 18:15:11.446][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.447][self$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[2025-06-09 18:15:11.447][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.447][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.447][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.448][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.448][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.448][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.448][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-09 18:15:11.449][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.449][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.449][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-09 18:15:11.449][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.450][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.450][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.450][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.450][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.450][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.450][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-09 18:15:11.450][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-09 18:15:11.451][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.451][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.452][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.452][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.453][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.453][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.453][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.453][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.454][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-09 18:15:11.454][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.454][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-09 18:15:11.455][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.455][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.455][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.455][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.456][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.456][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.456][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-09 18:15:11.456][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.457][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.457][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-09 18:15:11.457][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.457][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.458][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.458][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.458][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.458][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.458][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-09 18:15:11.458][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-09 18:15:11.458][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.459][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.460][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.460][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.460][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.460][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.461][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.461][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.461][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-09 18:15:11.462][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.462][self$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[2025-06-09 18:15:11.462][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.462][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.463][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.463][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.463][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.463][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.464][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-09 18:15:11.464][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.464][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.464][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-09 18:15:11.465][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.465][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.465][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.465][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.466][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.466][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.467][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.467][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.468][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.468][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.468][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.468][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.469][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-09 18:15:11.469][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.469][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-09 18:15:11.470][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.470][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.470][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.470][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.471][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.471][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.471][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-09 18:15:11.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.472][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.472][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-09 18:15:11.472][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.472][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.473][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.473][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.473][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-09 18:15:11.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.474][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.475][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.475][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.475][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.476][self$setPropertyValue]
biodb.DEBUG[2025-06-09 18:15:11.476][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:11.476][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.478][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[2025-06-09 18:15:11.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.481][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[2025-06-09 18:15:11.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.482][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[2025-06-09 18:15:11.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.484][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[2025-06-09 18:15:11.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.485][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[2025-06-09 18:15:11.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.486][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[2025-06-09 18:15:11.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.487][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[2025-06-09 18:15:11.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.489][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[2025-06-09 18:15:11.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.490][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[2025-06-09 18:15:11.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.492][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[2025-06-09 18:15:11.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.494][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[2025-06-09 18:15:11.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.495][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[2025-06-09 18:15:11.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.496][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[2025-06-09 18:15:11.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.497][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[2025-06-09 18:15:11.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.498][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[2025-06-09 18:15:11.498][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-09 18:15:11.499][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-09 18:15:11.499][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-09 18:15:11.499][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-09 18:15:11.500][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-09 18:15:11.500][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-09 18:15:11.500][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-09 18:15:11.501][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-09 18:15:11.501][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-09 18:15:11.502][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-09 18:15:11.502][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-09 18:15:11.502][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-09 18:15:11.503][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-09 18:15:11.503][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-09 18:15:11.503][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-09 18:15:11.504][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-09 18:15:11.504][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-09 18:15:11.504][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-09 18:15:11.505][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-09 18:15:11.505][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-09 18:15:11.506][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-09 18:15:11.506][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-09 18:15:11.506][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-09 18:15:11.507][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-09 18:15:11.507][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-09 18:15:11.507][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-09 18:15:11.508][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-09 18:15:11.508][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-09 18:15:11.509][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-09 18:15:11.509][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-09 18:15:11.509][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-09 18:15:11.510][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-09 18:15:11.510][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-09 18:15:11.510][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-09 18:15:11.511][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-09 18:15:11.511][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-09 18:15:11.511][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-09 18:15:11.512][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-09 18:15:11.512][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-09 18:15:11.513][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-09 18:15:11.513][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-09 18:15:11.513][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-09 18:15:11.514][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-09 18:15:11.514][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-09 18:15:11.514][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-09 18:15:11.515][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-09 18:15:11.515][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-09 18:15:11.515][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-09 18:15:11.516][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-09 18:15:11.516][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-09 18:15:11.517][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-09 18:15:11.517][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-09 18:15:11.517][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-09 18:15:11.518][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-09 18:15:11.518][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-09 18:15:11.518][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-09 18:15:11.519][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-09 18:15:11.519][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-09 18:15:11.519][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-09 18:15:11.520][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-09 18:15:11.520][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-09 18:15:11.520][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-09 18:15:11.521][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-09 18:15:11.521][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-09 18:15:11.521][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-09 18:15:11.522][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-09 18:15:11.522][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-09 18:15:11.523][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-09 18:15:11.523][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-09 18:15:11.523][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-09 18:15:11.524][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-09 18:15:11.524][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-09 18:15:11.524][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-09 18:15:11.525][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-09 18:15:11.525][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-09 18:15:11.525][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-09 18:15:11.526][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-09 18:15:11.526][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-09 18:15:11.527][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-09 18:15:11.527][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-09 18:15:11.527][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-09 18:15:11.528][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-09 18:15:11.528][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-09 18:15:11.528][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-09 18:15:11.529][initialize] This is biodb version 1.17.0.
biodb.DEBUG[2025-06-09 18:15:11.529][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-09 18:15:11.529][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.530][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.547][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[2025-06-09 18:15:11.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-09 18:15:11.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-09 18:15:11.557][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-06-09 18:15:11.557][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.558][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.558][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.558][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.559][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-09 18:15:11.559][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.559][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.560][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.560][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-06-09 18:15:11.560][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-09 18:15:11.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-06-09 18:15:11.561][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-06-09 18:15:11.562][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-09 18:15:11.562][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-09 18:15:11.562][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-09 18:15:11.562][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-09 18:15:11.562][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-09 18:15:11.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.563][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-09 18:15:11.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-09 18:15:11.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-09 18:15:11.564][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-09 18:15:11.564][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-06-09 18:15:11.564][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-06-09 18:15:11.564][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-09 18:15:11.564][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-09 18:15:11.565][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-09 18:15:11.565][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-06-09 18:15:11.565][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-06-09 18:15:11.565][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-09 18:15:11.566][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-09 18:15:11.566][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-06-09 18:15:11.566][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-09 18:15:11.567][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-09 18:15:11.567][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-09 18:15:11.568][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.569][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-06-09 18:15:11.569][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-06-09 18:15:11.569][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-06-09 18:15:11.570][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-06-09 18:15:11.570][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-06-09 18:15:11.570][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-06-09 18:15:11.570][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-06-09 18:15:11.571][biodb::testThat]
biodb.INFO [2025-06-09 18:15:11.571][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-06-09 18:15:11.571][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-09 18:15:11.572][biodb::testThat]
biodb.DEBUG[2025-06-09 18:15:11.573][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-06-09 18:15:11.574][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.574][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-06-09 18:15:11.575][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.575][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-06-09 18:15:11.576][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-06-09 18:15:11.577][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-06-09 18:15:11.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-06-09 18:15:11.578][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.581][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-06-09 18:15:11.582][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-06-09 18:15:11.582][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-06-09 18:15:11.583][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-06-09 18:15:11.583][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-06-09 18:15:11.584][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2025-06-09 18:15:11.585][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-06-09 18:15:11.585][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-06-09 18:15:11.585][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-06-09 18:15:11.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-09 18:15:11.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-09 18:15:11.590][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.590][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.591][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.592][ef$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:15:11.593][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:15:11.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.593][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.593][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-06-09 18:15:11.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-06-09 18:15:11.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.595][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:15:11.595][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:15:11.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.595][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-09 18:15:11.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-09 18:15:11.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.597][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-09 18:15:11.597][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-09 18:15:11.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.597][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.598][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-09 18:15:11.598][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-09 18:15:11.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.599][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.599][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:11.599][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:11.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.600][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.600][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:11.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-09 18:15:11.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.601][ef$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:15:11.601][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:15:11.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.602][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.602][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-06-09 18:15:11.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-09 18:15:11.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:11.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:11.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.604][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:11.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-09 18:15:11.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.605][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:11.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:11.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.606][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-09 18:15:11.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-09 18:15:11.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.608][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:15:11.608][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:15:11.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.608][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.609][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-06-09 18:15:11.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-06-09 18:15:11.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:15:11.610][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:15:11.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.611][ef$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-09 18:15:11.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-09 18:15:11.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:11.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:11.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:11.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:11.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-09 18:15:11.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-09 18:15:11.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-09 18:15:11.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-09 18:15:11.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-09 18:15:11.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-09 18:15:11.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-09 18:15:11.622][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-06-09 18:15:11.624][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-06-09 18:15:11.624][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-06-09 18:15:11.624][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-06-09 18:15:11.625][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-09 18:15:11.625][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-09 18:15:11.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-09 18:15:11.625][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-09 18:15:11.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-09 18:15:11.626][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-09 18:15:11.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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
ChebiConn0.6090.2310.844
ChebiEntry0.0780.0040.084