Back to Mac ARM64 build report for BioC 3.20
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-13 11:32:01 -0400 (Mon, 13 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4378
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 197/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: dfe3f6c
git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024)
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbChebi on kjohnson1


To the developers/maintainers of the biodbChebi package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biodbChebi
Version: 1.11.0
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_1.11.0.tar.gz
StartedAt: 2024-05-12 06:45:06 -0400 (Sun, 12 May 2024)
EndedAt: 2024-05-12 06:46:13 -0400 (Sun, 12 May 2024)
EllapsedTime: 66.5 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/biodbChebi.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* 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-3.20-bioc-mac-arm64/meat/biodbChebi.Rcheck/00check.log’
for details.

Installation output

biodbChebi.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-05-12 06:45:56.737][biodb::testContext]
biodb.INFO [2024-05-12 06:45:56.742][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-12 06:45:56.743][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-12 06:45:56.744][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-12 06:45:56.745][biodb::testContext]
biodb.INFO [2024-05-12 06:45:56.754][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-12 06:45:56.757][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-12 06:45:56.767][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:45:56.768][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-12 06:45:56.769][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-12 06:45:56.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.773][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-12 06:45:56.793][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-12 06:45:56.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.797][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-12 06:45:56.798][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-12 06:45:56.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.801][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-12 06:45:56.802][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-12 06:45:56.803][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-12 06:45:56.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.806][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-12 06:45:56.808][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-12 06:45:56.824][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-12 06:45:56.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.828][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-12 06:45:56.829][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-12 06:45:56.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.832][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-12 06:45:56.833][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-12 06:45:56.833][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-12 06:45:56.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.836][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-12 06:45:56.837][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-12 06:45:56.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.840][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-12 06:45:56.841][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-12 06:45:56.842][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-12 06:45:56.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.845][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-12 06:45:56.846][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-12 06:45:56.846][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-12 06:45:56.847][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-12 06:45:56.848][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-12 06:45:56.849][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-12 06:45:56.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.852][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-12 06:45:56.852][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-12 06:45:56.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.855][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-12 06:45:56.856][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-12 06:45:56.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.859][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-12 06:45:56.860][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-12 06:45:56.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.863][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-12 06:45:56.864][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-12 06:45:56.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.867][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-12 06:45:56.867][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-12 06:45:56.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.870][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-12 06:45:56.871][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-12 06:45:56.890][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-12 06:45:56.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.894][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-12 06:45:56.894][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-12 06:45:56.895][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-12 06:45:56.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:56.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:56.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:56.902][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-12 06:45:56.938][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:56.954][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-12 06:45:56.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:56.957][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:45:56.958][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:56.959][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:45:56.960][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:56.961][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:45:56.962][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-12 06:45:56.963][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:45:56.963][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:56.964][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-12 06:45:56.965][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:45:56.966][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:56.967][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:56.968][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:45:56.968][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:45:56.968][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:45:56.968][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-12 06:45:56.968][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-12 06:45:56.969][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:45:56.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:56.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:56.971][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:45:56.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:56.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:56.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:45:56.974][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:56.975][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:45:56.976][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:45:56.976][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:56.977][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:56.978][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-12 06:45:56.980][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:56.981][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-12 06:45:56.982][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:56.982][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:45:56.983][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:56.984][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:45:56.985][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:56.986][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:45:56.986][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-12 06:45:56.987][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:45:56.988][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:56.989][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-12 06:45:56.990][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:45:56.990][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:56.991][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:56.992][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:45:56.992][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:45:56.992][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:45:56.992][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-12 06:45:56.992][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-12 06:45:56.993][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:45:56.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:56.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:56.995][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:45:56.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:56.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:56.998][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:45:56.998][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:56.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:45:57.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:45:57.001][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.001][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.003][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-12 06:45:57.005][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.006][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-12 06:45:57.007][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.008][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:45:57.009][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.010][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.010][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.011][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.012][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-12 06:45:57.013][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:45:57.014][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.015][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-12 06:45:57.016][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:45:57.016][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.017][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.018][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.026][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:45:57.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:57.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:57.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:45:57.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:57.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:57.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.032][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:45:57.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:45:57.034][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.035][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.036][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-12 06:45:57.037][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.038][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-12 06:45:57.039][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.040][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:45:57.041][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.042][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.042][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.043][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.044][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-12 06:45:57.045][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:45:57.046][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.046][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-12 06:45:57.047][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:45:57.048][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.049][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.050][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.050][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:45:57.051][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:57.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:57.053][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:45:57.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:57.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:57.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.056][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.057][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:45:57.057][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:45:57.058][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.059][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:45:57.064][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:45:57.065][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.066][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[2024-05-12 06:45:57.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.070][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[2024-05-12 06:45:57.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.114][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[2024-05-12 06:45:57.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.117][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[2024-05-12 06:45:57.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.128][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[2024-05-12 06:45:57.129][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-12 06:45:57.135][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-12 06:45:57.136][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-12 06:45:57.137][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-12 06:45:57.139][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-12 06:45:57.140][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-12 06:45:57.141][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-12 06:45:57.142][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-12 06:45:57.143][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-12 06:45:57.144][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-12 06:45:57.146][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-12 06:45:57.147][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-12 06:45:57.148][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-12 06:45:57.149][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-12 06:45:57.150][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-12 06:45:57.151][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-12 06:45:57.152][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-12 06:45:57.154][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-12 06:45:57.155][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-12 06:45:57.156][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-12 06:45:57.157][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-12 06:45:57.158][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-12 06:45:57.160][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-12 06:45:57.161][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-12 06:45:57.162][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-12 06:45:57.163][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-12 06:45:57.164][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-12 06:45:57.166][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-12 06:45:57.167][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-12 06:45:57.168][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-12 06:45:57.169][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-12 06:45:57.171][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-12 06:45:57.172][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-12 06:45:57.173][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-12 06:45:57.174][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-12 06:45:57.175][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-12 06:45:57.177][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-12 06:45:57.178][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-12 06:45:57.179][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-12 06:45:57.180][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-12 06:45:57.181][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-12 06:45:57.183][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-12 06:45:57.184][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-12 06:45:57.185][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-12 06:45:57.187][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-12 06:45:57.188][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-12 06:45:57.189][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-12 06:45:57.191][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-12 06:45:57.192][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-12 06:45:57.193][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-12 06:45:57.195][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-12 06:45:57.203][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-12 06:45:57.204][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-12 06:45:57.205][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-12 06:45:57.206][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-12 06:45:57.208][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-12 06:45:57.209][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-12 06:45:57.210][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-12 06:45:57.211][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-12 06:45:57.212][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-12 06:45:57.213][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-12 06:45:57.215][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-12 06:45:57.216][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-12 06:45:57.217][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-12 06:45:57.218][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-12 06:45:57.220][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-12 06:45:57.221][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-12 06:45:57.223][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-12 06:45:57.224][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-12 06:45:57.225][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-12 06:45:57.226][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-12 06:45:57.227][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-12 06:45:57.229][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-12 06:45:57.230][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-12 06:45:57.231][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-12 06:45:57.232][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-12 06:45:57.234][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-12 06:45:57.236][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-12 06:45:57.237][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-12 06:45:57.238][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-12 06:45:57.239][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-12 06:45:57.240][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-12 06:45:57.241][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-12 06:45:57.247][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-12 06:45:57.249][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-12 06:45:57.254][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:45:57.255][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.256][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.286][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[2024-05-12 06:45:57.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.296][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[2024-05-12 06:45:57.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.314][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[2024-05-12 06:45:57.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.319][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[2024-05-12 06:45:57.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:45:57.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:45:57.352][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-12 06:45:57.363][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-12 06:45:57.365][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.366][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.367][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:45:57.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.370][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.371][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.377][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-12 06:45:57.379][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-12 06:45:57.380][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:45:57.381][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.381][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-12 06:45:57.382][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-12 06:45:57.383][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-12 06:45:57.384][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-12 06:45:57.385][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:45:57.385][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:45:57.385][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:45:57.386][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-12 06:45:57.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:57.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:57.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:45:57.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:45:57.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:45:57.390][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:45:57.391][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-12 06:45:57.391][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-12 06:45:57.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:45:57.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:45:57.394][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-12 06:45:57.394][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-12 06:45:57.394][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-12 06:45:57.400][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-12 06:45:57.402][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-12 06:45:57.404][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-12 06:45:57.405][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-12 06:45:57.407][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-12 06:45:57.408][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-12 06:45:57.442][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-12 06:45:57.444][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-12 06:45:57.449][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-12 06:45:57.455][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-12 06:45:57.460][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-12 06:45:57.461][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-12 06:45:57.463][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-12 06:45:57.463][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-12 06:45:57.477][biodb::testThat]
biodb.INFO [2024-05-12 06:45:57.478][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-12 06:45:57.479][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:57.479][biodb::testThat]
biodb.TRACE[2024-05-12 06:45:57.484][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-05-12 06:45:57.487][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-12 06:45:57.491][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-12 06:45:57.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:45:57.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:57.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:57.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:57.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:57.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:57.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-12 06:45:57.537][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.538][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.540][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.558][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:57.559][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:57.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.561][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.588][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:57.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:57.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.592][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:57.593][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:57.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.594][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:57.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:57.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.599][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:57.600][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:57.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.601][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:57.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:57.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.606][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:57.607][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:57.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.608][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:57.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:57.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.625][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:57.626][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:57.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.628][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.629][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:57.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:57.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.633][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:45:57.633][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:57.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.635][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.636][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:45:57.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.640][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:57.640][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:57.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.642][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:57.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:57.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.647][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:57.647][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:57.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.649][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:57.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:57.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.654][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:45:57.655][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:57.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.657][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.658][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:45:57.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:57.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.662][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:57.663][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:57.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.664][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.665][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:57.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:57.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-12 06:45:57.736][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-05-12 06:45:57.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:57.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:57.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:57.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:57.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:57.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:57.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:57.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:57.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:57.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:57.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:57.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:57.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.835][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-12 06:45:57.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-12 06:45:57.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.839][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-12 06:45:57.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-12 06:45:57.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.842][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-12 06:45:57.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-12 06:45:57.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-12 06:45:57.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-12 06:45:57.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.954][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.955][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.957][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:57.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:57.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.989][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.990][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:57.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:57.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:57.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:58.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:58.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:58.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:58.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:58.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:58.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.013][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:58.014][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:58.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.015][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:58.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:58.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.028][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:58.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:58.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:58.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:58.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.035][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:58.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:58.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.038][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:58.039][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:58.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.041][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:58.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:58.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.064][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.064][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.066][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.088][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.089][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.091][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.103][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:58.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:58.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.107][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:58.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:58.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.110][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:58.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:58.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.113][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:58.114][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:58.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.116][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.117][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:58.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:58.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.128][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.132][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.142][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.146][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.147][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.149][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.149][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.161][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.165][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.169][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.172][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.173][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.174][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.175][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.187][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:58.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:58.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.191][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:58.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:58.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:58.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:58.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.198][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:58.199][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:58.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.201][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:58.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:58.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.224][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.225][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.227][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:58.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:58.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:58.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:58.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:58.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:58.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.249][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:58.250][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:58.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.252][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:58.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:58.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.265][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.266][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.268][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.273][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:58.274][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:58.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.276][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.282][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:58.283][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:58.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.285][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.289][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:58.291][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:58.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.292][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.298][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.299][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.308][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.313][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.314][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.321][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.322][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.324][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.329][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.330][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.337][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.338][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.340][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.345][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:58.346][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:58.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.348][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.354][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:58.355][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:58.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.356][ef$get] fields variable is a list.
biodb.INFO [2024-05-12 06:45:58.365][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.366][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-12 06:45:58.367][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:58.368][biodb::testThat]
biodb.DEBUG[2024-05-12 06:45:58.382][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-05-12 06:45:58.392][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-12 06:45:58.397][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-05-12 06:45:58.398][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:45:58.399][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-05-12 06:45:58.400][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-12 06:45:58.424][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-12 06:45:58.425][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-12 06:45:58.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:45:58.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:45:58.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:45:58.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:45:58.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:45:58.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:45:58.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-12 06:45:58.439][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.440][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.442][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.463][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:45:58.464][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:45:58.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.466][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.475][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:45:58.476][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:45:58.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.480][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:45:58.481][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:45:58.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.483][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.484][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.485][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:45:58.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.486][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.488][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.489][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:45:58.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.490][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.491][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:45:58.492][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:45:58.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.494][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.495][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.496][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:58.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.498][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:58.499][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:58.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.501][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.502][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:45:58.503][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:45:58.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.505][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.506][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:45:58.506][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:45:58.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.508][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:58.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:58.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:58.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:58.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:45:58.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:45:58.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:58.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:45:58.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:45:58.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-12 06:45:58.544][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-12 06:45:58.544][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-12 06:45:58.568][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.569][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-12 06:45:58.570][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:58.571][biodb::testThat]
biodb.TRACE[2024-05-12 06:45:58.574][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:58.576][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:58.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:58.577][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-12 06:45:58.579][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.INFO [2024-05-12 06:45:58.815][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.816][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-12 06:45:58.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:58.818][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.883][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.884][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-12 06:45:58.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:58.886][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.943][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.944][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-12 06:45:58.945][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:58.946][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.955][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.956][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-12 06:45:58.957][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:58.958][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.968][biodb::testThat]
biodb.INFO [2024-05-12 06:45:58.969][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-12 06:45:58.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:58.970][biodb::testThat]
biodb.DEBUG[2024-05-12 06:45:58.975][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-05-12 06:45:59.314][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-05-12 06:45:59.638][biodb::testThat]
biodb.INFO [2024-05-12 06:45:59.640][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-12 06:45:59.641][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:59.641][biodb::testThat]
biodb.DEBUG[2024-05-12 06:45:59.754][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-05-12 06:45:59.872][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:45:59.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:45:59.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:59.875][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:45:59.876][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:59.877][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:45:59.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:45:59.879][ef$get] fields variable is a list.
biodb.INFO [2024-05-12 06:45:59.881][biodb::testThat]
biodb.INFO [2024-05-12 06:45:59.882][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-12 06:45:59.882][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:59.883][biodb::testThat]
biodb.INFO [2024-05-12 06:45:59.981][biodb::testThat]
biodb.INFO [2024-05-12 06:45:59.982][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-12 06:45:59.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:45:59.984][biodb::testThat]
biodb.INFO [2024-05-12 06:46:00.016][biodb::testThat]
biodb.INFO [2024-05-12 06:46:00.017][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-12 06:46:00.018][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:00.018][biodb::testThat]
biodb.INFO [2024-05-12 06:46:00.037][biodb::testThat]
biodb.INFO [2024-05-12 06:46:00.038][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-12 06:46:00.039][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:00.039][biodb::testThat]
biodb.INFO [2024-05-12 06:46:00.058][biodb::testThat]
biodb.INFO [2024-05-12 06:46:00.059][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-12 06:46:00.060][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:00.061][biodb::testThat]
biodb.DEBUG[2024-05-12 06:46:00.063][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-12 06:46:00.341][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-12 06:46:00.357][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-12 06:46:00.361][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:00.363][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2024-05-12 06:46:00.365][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-12 06:46:00.366][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-12 06:46:00.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-12 06:46:00.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:00.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:00.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:00.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:00.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:00.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:00.378][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.TRACE[2024-05-12 06:46:00.382][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.383][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.384][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.389][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:46:00.390][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:46:00.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.392][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.393][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:46:00.394][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:46:00.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.396][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.398][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:46:00.399][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:46:00.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.400][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.402][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.403][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.404][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.406][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.407][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.408][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.410][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:46:00.411][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:46:00.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.412][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.413][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.414][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.416][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.417][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:00.418][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:00.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.420][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.421][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:46:00.422][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:46:00.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.424][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.425][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:46:00.426][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:46:00.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.428][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-12 06:46:00.502][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-12 06:46:00.502][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-12 06:46:00.522][biodb::testThat]
biodb.INFO [2024-05-12 06:46:00.523][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-12 06:46:00.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:00.525][biodb::testThat]
biodb.DEBUG[2024-05-12 06:46:00.538][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-05-12 06:46:00.540][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-05-12 06:46:00.541][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-12 06:46:00.543][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-05-12 06:46:00.545][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-05-12 06:46:00.548][loadFileContents] Loaded 3 files from cache: [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2024-05-12 06:46:00.549][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-12 06:46:00.551][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-05-12 06:46:00.552][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-05-12 06:46:00.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:00.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:00.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:00.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:00.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:00.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:00.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-12 06:46:00.567][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.569][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.571][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.577][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:46:00.578][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:46:00.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.580][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.581][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:46:00.582][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:46:00.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.584][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.585][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:46:00.586][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:46:00.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.589][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.590][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.592][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.594][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.596][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.598][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.599][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:46:00.600][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:46:00.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.602][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.606][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.607][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:00.608][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:00.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.610][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.611][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:46:00.612][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:46:00.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.614][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.615][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:46:00.616][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:46:00.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.618][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-12 06:46:00.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:00.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:00.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:00.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:00.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:00.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:00.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-12 06:46:00.658][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.660][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.661][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.667][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:46:00.668][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:46:00.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.670][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.671][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:46:00.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:46:00.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.675][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:46:00.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:46:00.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.678][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.679][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:46:00.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:46:00.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.683][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:46:00.684][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:46:00.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.695][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:46:00.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:46:00.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.702][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.703][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.709][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.710][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.712][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.713][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.717][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:46:00.718][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:46:00.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.719][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.721][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:46:00.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:46:00.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.724][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.725][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.727][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.734][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:00.735][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:00.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.738][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:00.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:00.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.744][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:46:00.745][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:46:00.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.746][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.747][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:46:00.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:46:00.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.751][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:46:00.752][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:46:00.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.753][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.754][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:46:00.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:46:00.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-12 06:46:00.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:00.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:00.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:00.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:00.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:00.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:00.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-12 06:46:00.795][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.796][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.798][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.803][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:46:00.804][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:46:00.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.806][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:46:00.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:46:00.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.812][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:46:00.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:46:00.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.815][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:46:00.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:46:00.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.819][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:46:00.820][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:46:00.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:46:00.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:46:00.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.827][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.829][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:46:00.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.834][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.835][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.836][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.837][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:00.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.841][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:46:00.842][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:46:00.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.843][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.845][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:46:00.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:46:00.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.848][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.849][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.851][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:00.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.855][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:00.856][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:00.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.858][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:00.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:00.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.863][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:46:00.864][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:46:00.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.865][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.866][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:46:00.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:46:00.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.870][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:46:00.871][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:46:00.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.872][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.873][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:46:00.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:46:00.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:00.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:00.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:00.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:00.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:00.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-12 06:46:00.932][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-05-12 06:46:00.933][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-12 06:46:00.934][function(conn, opt)] Entries: [4]: "NULL, NULL, <environment>, <environment>"
biodb.INFO [2024-05-12 06:46:00.972][biodb::testThat]
biodb.INFO [2024-05-12 06:46:00.973][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-12 06:46:00.974][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:00.975][biodb::testThat]
biodb.INFO [2024-05-12 06:46:01.023][biodb::testThat]
biodb.INFO [2024-05-12 06:46:01.025][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-12 06:46:01.026][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:01.027][biodb::testThat]
biodb.INFO [2024-05-12 06:46:01.036][biodb::testThat]
biodb.INFO [2024-05-12 06:46:01.037][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-12 06:46:01.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:01.039][biodb::testThat]
biodb.DEBUG[2024-05-12 06:46:01.045][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-12 06:46:01.067][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:01.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-12 06:46:01.078][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:01.080][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-12 06:46:01.103][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:01.106][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:01.108][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2024-05-12 06:46:01.109][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:01.112][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2024-05-12 06:46:01.125][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:01.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:01.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:01.128][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:01.129][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:01.130][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:01.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:01.131][ef$get] fields variable is a list.
biodb.INFO [2024-05-12 06:46:01.133][biodb::testThat]
biodb.INFO [2024-05-12 06:46:01.134][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-12 06:46:01.135][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:01.135][biodb::testThat]
biodb.ERROR[2024-05-12 06:46:01.207][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-12 06:46:01.226][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-12 06:46:01.241][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-12 06:46:01.243][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-12 06:46:01.244][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-12 06:46:01.245][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-12 06:46:01.245][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.247][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.248][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-12 06:46:01.260][biodb::testContext]
biodb.INFO [2024-05-12 06:46:01.261][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-12 06:46:01.262][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-05-12 06:46:01.263][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-12 06:46:01.264][biodb::testContext]
biodb.INFO [2024-05-12 06:46:01.266][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-12 06:46:01.267][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-12 06:46:01.272][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:01.273][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-12 06:46:01.274][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-12 06:46:01.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.277][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-12 06:46:01.278][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-12 06:46:01.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.281][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-12 06:46:01.282][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-12 06:46:01.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.285][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-12 06:46:01.286][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-12 06:46:01.287][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-12 06:46:01.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.290][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-12 06:46:01.291][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-12 06:46:01.292][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-12 06:46:01.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.295][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-12 06:46:01.296][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-12 06:46:01.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.299][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-12 06:46:01.299][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-12 06:46:01.300][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-12 06:46:01.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.303][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-12 06:46:01.304][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-12 06:46:01.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.307][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-12 06:46:01.308][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-12 06:46:01.309][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-12 06:46:01.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.311][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-12 06:46:01.312][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-12 06:46:01.313][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-12 06:46:01.314][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-12 06:46:01.315][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-12 06:46:01.316][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-12 06:46:01.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.319][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-12 06:46:01.319][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-12 06:46:01.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.322][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-12 06:46:01.323][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-12 06:46:01.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.326][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-12 06:46:01.327][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-12 06:46:01.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.330][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-12 06:46:01.331][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-12 06:46:01.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.334][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-12 06:46:01.335][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-12 06:46:01.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.338][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-12 06:46:01.338][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-12 06:46:01.355][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-12 06:46:01.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.359][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-12 06:46:01.360][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-12 06:46:01.361][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-12 06:46:01.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.364][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-12 06:46:01.366][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.367][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-12 06:46:01.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.369][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:01.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.370][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.371][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.373][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-12 06:46:01.374][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:01.374][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.375][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-12 06:46:01.376][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:01.377][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.378][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.379][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:01.379][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:01.379][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:01.379][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-12 06:46:01.379][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-12 06:46:01.380][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:01.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:01.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.384][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.385][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:01.387][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:01.388][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.388][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.389][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-12 06:46:01.391][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.392][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-12 06:46:01.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:01.395][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.396][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.396][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.397][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.398][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-12 06:46:01.399][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:01.400][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.401][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-12 06:46:01.401][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:01.402][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.403][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.404][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:01.404][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:01.404][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:01.404][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-12 06:46:01.404][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-12 06:46:01.405][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:01.405][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.407][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:01.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.409][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.410][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.411][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:01.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:01.413][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.414][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.415][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-12 06:46:01.417][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.418][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-12 06:46:01.420][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.421][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:01.422][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.424][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.425][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.427][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-12 06:46:01.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:01.430][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.431][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-12 06:46:01.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:01.432][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.434][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.435][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:01.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:01.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.439][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.440][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.441][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:01.441][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:01.442][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.451][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.456][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-12 06:46:01.458][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.459][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-12 06:46:01.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:01.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.462][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.463][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.464][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.465][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-12 06:46:01.466][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:01.466][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.467][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-12 06:46:01.468][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:01.469][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.470][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.471][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.471][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:01.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:01.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.476][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.477][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:01.478][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:01.479][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.480][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:01.481][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:01.482][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.542][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[2024-05-12 06:46:01.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.547][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-12 06:46:01.548][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-12 06:46:01.549][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-12 06:46:01.551][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-12 06:46:01.552][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-12 06:46:01.553][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-12 06:46:01.554][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-12 06:46:01.555][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-12 06:46:01.556][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-12 06:46:01.557][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-12 06:46:01.559][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-12 06:46:01.560][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-12 06:46:01.561][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-12 06:46:01.562][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-12 06:46:01.563][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-12 06:46:01.564][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-12 06:46:01.565][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-12 06:46:01.566][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-12 06:46:01.568][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-12 06:46:01.570][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-12 06:46:01.571][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-12 06:46:01.573][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-12 06:46:01.574][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-12 06:46:01.575][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-12 06:46:01.576][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-12 06:46:01.577][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-12 06:46:01.579][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-12 06:46:01.580][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-12 06:46:01.581][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-12 06:46:01.582][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-12 06:46:01.583][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-12 06:46:01.585][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-12 06:46:01.586][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-12 06:46:01.587][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-12 06:46:01.588][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-12 06:46:01.589][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-12 06:46:01.590][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-12 06:46:01.592][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-12 06:46:01.593][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-12 06:46:01.594][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-12 06:46:01.595][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-12 06:46:01.596][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-12 06:46:01.597][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-12 06:46:01.599][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-12 06:46:01.600][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-12 06:46:01.601][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-12 06:46:01.602][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-12 06:46:01.603][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-12 06:46:01.605][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-12 06:46:01.606][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-12 06:46:01.607][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-12 06:46:01.608][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-12 06:46:01.609][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-12 06:46:01.610][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-12 06:46:01.612][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-12 06:46:01.613][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-12 06:46:01.614][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-12 06:46:01.615][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-12 06:46:01.616][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-12 06:46:01.617][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-12 06:46:01.618][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-12 06:46:01.620][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-12 06:46:01.621][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-12 06:46:01.622][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-12 06:46:01.623][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-12 06:46:01.624][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-12 06:46:01.625][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-12 06:46:01.627][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-12 06:46:01.628][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-12 06:46:01.629][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-12 06:46:01.630][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-12 06:46:01.631][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-12 06:46:01.633][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-12 06:46:01.634][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-12 06:46:01.635][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-12 06:46:01.637][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-12 06:46:01.638][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-12 06:46:01.639][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-12 06:46:01.641][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-12 06:46:01.642][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-12 06:46:01.643][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-12 06:46:01.644][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-12 06:46:01.645][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-12 06:46:01.647][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-12 06:46:01.648][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-12 06:46:01.650][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:01.650][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.652][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:01.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.740][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-12 06:46:01.742][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-12 06:46:01.744][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.745][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.747][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:01.748][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.748][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.749][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.750][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-12 06:46:01.751][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-12 06:46:01.752][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:01.753][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.754][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-12 06:46:01.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-12 06:46:01.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-12 06:46:01.757][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:01.758][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:01.758][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:01.758][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:01.758][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-12 06:46:01.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.761][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:01.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:01.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:01.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:01.765][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-12 06:46:01.765][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-12 06:46:01.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:01.767][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:01.768][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:01.777][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-12 06:46:01.777][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-12 06:46:01.778][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-12 06:46:01.779][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-12 06:46:01.781][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-12 06:46:01.782][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-12 06:46:01.784][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-12 06:46:01.785][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-12 06:46:01.788][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-12 06:46:01.789][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-12 06:46:01.791][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-12 06:46:01.792][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-12 06:46:01.793][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-12 06:46:01.794][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-12 06:46:01.795][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-12 06:46:01.796][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-12 06:46:01.797][biodb::testThat]
biodb.INFO [2024-05-12 06:46:01.798][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-05-12 06:46:01.799][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:01.799][biodb::testThat]
biodb.DEBUG[2024-05-12 06:46:01.803][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-12 06:46:01.807][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:01.808][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-12 06:46:01.809][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:01.811][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-12 06:46:01.814][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:01.817][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:01.833][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-12 06:46:01.834][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:01.836][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-12 06:46:01.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:01.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.867][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:01.871][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:01.873][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-12 06:46:01.874][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:01.876][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-12 06:46:01.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:01.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:01.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.920][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:01.923][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:01.925][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-12 06:46:01.926][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:01.927][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-12 06:46:01.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:01.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.940][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:01.943][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:01.945][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-12 06:46:01.946][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:01.947][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-12 06:46:01.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:01.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:01.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.975][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:01.978][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:01.979][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-12 06:46:01.980][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:01.982][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-12 06:46:01.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:01.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:01.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:01.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:01.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:01.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:01.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:01.996][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:02.000][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:02.001][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-12 06:46:02.002][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:02.004][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-12 06:46:02.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:02.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.017][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:02.021][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:02.022][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-05-12 06:46:02.023][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:02.025][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-05-12 06:46:02.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:02.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-12 06:46:02.044][biodb::testThat]
biodb.INFO [2024-05-12 06:46:02.045][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-05-12 06:46:02.046][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:02.047][biodb::testThat]
biodb.DEBUG[2024-05-12 06:46:02.050][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:02.054][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:02.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2024-05-12 06:46:02.057][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:02.059][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2024-05-12 06:46:02.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:02.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.075][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:02.079][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:02.080][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2024-05-12 06:46:02.082][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:02.083][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2024-05-12 06:46:02.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:02.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-12 06:46:02.101][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-12 06:46:02.103][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-12 06:46:02.104][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-12 06:46:02.105][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-12 06:46:02.105][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.107][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.108][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-12 06:46:02.113][biodb::testContext]
biodb.INFO [2024-05-12 06:46:02.114][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-12 06:46:02.115][biodb::testContext] Test context - Test web services
biodb.INFO [2024-05-12 06:46:02.116][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-12 06:46:02.116][biodb::testContext]
biodb.INFO [2024-05-12 06:46:02.119][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-12 06:46:02.121][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-12 06:46:02.126][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:02.127][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-12 06:46:02.128][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.131][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[2024-05-12 06:46:02.132][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-12 06:46:02.133][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.136][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-12 06:46:02.137][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.140][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-12 06:46:02.141][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-12 06:46:02.142][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-12 06:46:02.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.145][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-12 06:46:02.145][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-12 06:46:02.146][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.149][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-12 06:46:02.150][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-12 06:46:02.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.153][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-12 06:46:02.154][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-12 06:46:02.155][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-12 06:46:02.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.157][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-12 06:46:02.158][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.161][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-12 06:46:02.162][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-12 06:46:02.163][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.166][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-12 06:46:02.167][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-12 06:46:02.167][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-12 06:46:02.168][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-12 06:46:02.169][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-12 06:46:02.170][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-12 06:46:02.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.182][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-12 06:46:02.183][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-12 06:46:02.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.185][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[2024-05-12 06:46:02.186][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-12 06:46:02.187][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-12 06:46:02.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.190][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-12 06:46:02.191][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-12 06:46:02.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.194][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-12 06:46:02.195][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-12 06:46:02.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.198][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-12 06:46:02.198][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-12 06:46:02.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.200][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[2024-05-12 06:46:02.201][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-12 06:46:02.202][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-12 06:46:02.219][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-12 06:46:02.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.223][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-12 06:46:02.224][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-12 06:46:02.224][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-12 06:46:02.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.228][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-12 06:46:02.229][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.230][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-12 06:46:02.231][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.232][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.233][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.233][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.234][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.235][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.236][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-12 06:46:02.237][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.237][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.238][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-12 06:46:02.239][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.240][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.240][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.241][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:02.241][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:02.241][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:02.241][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-12 06:46:02.241][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-12 06:46:02.242][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:02.243][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.244][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.246][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.247][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.248][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.249][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.249][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.250][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.251][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-12 06:46:02.253][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.254][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-12 06:46:02.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.256][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.257][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.258][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.259][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.259][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-12 06:46:02.260][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.261][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.262][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-12 06:46:02.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.263][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.264][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.265][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:02.265][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:02.265][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:02.265][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-12 06:46:02.265][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-12 06:46:02.266][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:02.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.268][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.270][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.271][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.272][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.273][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.274][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.274][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.276][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-12 06:46:02.277][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.278][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-12 06:46:02.279][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.280][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.281][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.282][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.282][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.283][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.284][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-12 06:46:02.285][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.286][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.287][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-12 06:46:02.288][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.288][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.289][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.290][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.291][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:02.292][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.293][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.294][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.295][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.295][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.296][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.297][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.298][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.299][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.299][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.300][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-12 06:46:02.302][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.303][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-12 06:46:02.304][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.305][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.306][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.307][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.307][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.308][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.309][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-12 06:46:02.310][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.311][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.311][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-12 06:46:02.312][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.313][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.314][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.315][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.315][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:02.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.321][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.322][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.323][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.324][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.325][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:02.326][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.360][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[2024-05-12 06:46:02.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.364][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[2024-05-12 06:46:02.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.372][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[2024-05-12 06:46:02.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.392][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-12 06:46:02.393][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-12 06:46:02.394][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-12 06:46:02.395][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-12 06:46:02.397][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-12 06:46:02.398][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-12 06:46:02.399][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-12 06:46:02.400][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-12 06:46:02.401][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-12 06:46:02.402][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-12 06:46:02.403][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-12 06:46:02.405][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-12 06:46:02.406][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-12 06:46:02.407][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-12 06:46:02.408][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-12 06:46:02.409][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-12 06:46:02.410][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-12 06:46:02.412][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-12 06:46:02.413][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-12 06:46:02.414][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-12 06:46:02.415][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-12 06:46:02.416][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-12 06:46:02.417][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-12 06:46:02.419][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-12 06:46:02.420][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-12 06:46:02.421][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-12 06:46:02.422][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-12 06:46:02.423][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-12 06:46:02.424][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-12 06:46:02.426][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-12 06:46:02.427][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-12 06:46:02.428][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-12 06:46:02.429][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-12 06:46:02.430][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-12 06:46:02.431][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-12 06:46:02.433][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-12 06:46:02.434][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-12 06:46:02.435][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-12 06:46:02.436][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-12 06:46:02.438][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-12 06:46:02.439][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-12 06:46:02.440][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-12 06:46:02.441][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-12 06:46:02.442][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-12 06:46:02.443][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-12 06:46:02.444][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-12 06:46:02.446][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-12 06:46:02.447][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-12 06:46:02.448][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-12 06:46:02.449][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-12 06:46:02.450][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-12 06:46:02.452][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-12 06:46:02.453][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-12 06:46:02.454][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-12 06:46:02.455][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-12 06:46:02.457][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-12 06:46:02.458][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-12 06:46:02.459][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-12 06:46:02.460][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-12 06:46:02.461][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-12 06:46:02.462][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-12 06:46:02.464][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-12 06:46:02.465][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-12 06:46:02.466][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-12 06:46:02.467][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-12 06:46:02.468][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-12 06:46:02.469][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-12 06:46:02.470][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-12 06:46:02.472][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-12 06:46:02.473][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-12 06:46:02.474][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-12 06:46:02.475][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-12 06:46:02.476][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-12 06:46:02.477][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-12 06:46:02.478][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-12 06:46:02.480][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-12 06:46:02.481][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-12 06:46:02.482][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-12 06:46:02.483][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-12 06:46:02.484][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-12 06:46:02.485][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-12 06:46:02.486][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-12 06:46:02.488][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-12 06:46:02.489][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-12 06:46:02.491][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-12 06:46:02.492][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:02.492][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.494][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.532][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[2024-05-12 06:46:02.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.542][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[2024-05-12 06:46:02.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.594][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-12 06:46:02.596][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-12 06:46:02.599][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.600][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.601][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.602][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.603][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.604][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.605][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.606][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-12 06:46:02.607][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-12 06:46:02.608][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.609][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.609][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-12 06:46:02.610][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-12 06:46:02.611][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-12 06:46:02.613][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.614][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:02.614][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:02.614][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:02.615][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-12 06:46:02.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.617][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.618][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.619][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.620][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.621][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-12 06:46:02.621][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-12 06:46:02.622][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.623][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.624][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.624][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-12 06:46:02.624][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-12 06:46:02.626][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-12 06:46:02.627][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-12 06:46:02.628][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-12 06:46:02.630][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-12 06:46:02.631][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-12 06:46:02.633][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-12 06:46:02.636][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-12 06:46:02.637][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-12 06:46:02.638][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-12 06:46:02.640][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-12 06:46:02.641][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-12 06:46:02.642][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-12 06:46:02.643][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-12 06:46:02.644][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-12 06:46:02.645][biodb::testThat]
biodb.INFO [2024-05-12 06:46:02.646][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-05-12 06:46:02.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:02.648][biodb::testThat]
biodb.DEBUG[2024-05-12 06:46:02.651][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-12 06:46:02.655][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:02.656][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-12 06:46:02.658][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:02.659][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-12 06:46:02.663][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:02.666][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:02.668][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-12 06:46:02.669][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:02.671][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2024-05-12 06:46:02.680][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-12 06:46:02.681][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-12 06:46:02.682][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-12 06:46:02.683][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-12 06:46:02.684][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:02.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:02.685][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.687][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-12 06:46:02.691][biodb::testContext]
biodb.INFO [2024-05-12 06:46:02.692][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-12 06:46:02.693][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-05-12 06:46:02.694][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-12 06:46:02.695][biodb::testContext]
biodb.INFO [2024-05-12 06:46:02.697][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-12 06:46:02.699][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-12 06:46:02.704][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:02.705][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-12 06:46:02.706][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.709][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-12 06:46:02.709][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.712][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-12 06:46:02.713][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.716][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-12 06:46:02.717][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-12 06:46:02.718][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-12 06:46:02.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.721][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-12 06:46:02.722][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-12 06:46:02.722][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.725][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-12 06:46:02.726][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-12 06:46:02.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.729][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-12 06:46:02.730][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-12 06:46:02.731][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-12 06:46:02.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.733][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-12 06:46:02.734][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.737][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-12 06:46:02.738][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-12 06:46:02.739][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-12 06:46:02.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.741][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-12 06:46:02.742][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-12 06:46:02.743][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-12 06:46:02.744][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-12 06:46:02.745][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-12 06:46:02.745][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-12 06:46:02.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.748][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-12 06:46:02.749][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-12 06:46:02.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.752][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-12 06:46:02.753][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-12 06:46:02.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.756][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-12 06:46:02.756][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-12 06:46:02.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.759][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-12 06:46:02.760][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-12 06:46:02.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.763][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-12 06:46:02.764][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-12 06:46:02.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.767][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-12 06:46:02.767][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-12 06:46:02.781][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-12 06:46:02.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.785][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-12 06:46:02.786][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-12 06:46:02.787][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-12 06:46:02.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.790][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-12 06:46:02.792][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.793][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-12 06:46:02.794][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.794][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.795][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.796][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.797][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.798][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.799][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-12 06:46:02.799][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.800][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.801][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-12 06:46:02.802][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.803][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.803][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.804][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:02.804][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:02.804][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:02.804][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-12 06:46:02.804][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-12 06:46:02.805][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:02.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.808][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.811][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.812][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.812][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.813][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.814][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.815][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.816][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-12 06:46:02.818][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.819][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-12 06:46:02.820][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.821][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.822][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.823][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.824][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.824][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.825][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-12 06:46:02.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.827][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.828][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-12 06:46:02.828][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.829][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.830][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.831][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:02.831][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:02.831][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:02.831][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-12 06:46:02.831][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-12 06:46:02.832][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:02.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.836][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.837][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.838][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.839][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.839][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.840][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.841][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-12 06:46:02.843][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.844][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-12 06:46:02.845][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.846][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.846][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.847][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.848][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.850][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.851][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-12 06:46:02.852][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.853][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.853][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-12 06:46:02.854][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.855][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.856][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.857][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.858][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:02.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.860][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.869][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.871][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.872][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.872][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.873][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.874][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.875][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.876][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-12 06:46:02.877][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.878][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-12 06:46:02.879][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.880][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:02.881][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.881][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.882][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.883][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.884][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-12 06:46:02.885][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:02.886][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.886][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-12 06:46:02.887][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:02.888][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.889][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:02.890][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.891][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-12 06:46:02.891][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.893][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:02.894][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:02.895][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:02.895][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:02.896][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.897][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:02.898][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:02.899][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:02.900][self$setPropertyValue]
biodb.DEBUG[2024-05-12 06:46:02.901][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:02.902][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:02.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:02.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:02.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:02.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:02.970][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-12 06:46:02.972][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-12 06:46:02.973][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-12 06:46:02.974][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-12 06:46:02.975][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-12 06:46:02.977][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-12 06:46:02.978][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-12 06:46:02.979][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-12 06:46:02.980][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-12 06:46:02.981][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-12 06:46:02.982][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-12 06:46:02.984][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-12 06:46:02.985][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-12 06:46:02.986][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-12 06:46:02.987][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-12 06:46:02.988][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-12 06:46:02.990][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-12 06:46:02.991][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-12 06:46:02.992][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-12 06:46:02.993][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-12 06:46:02.994][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-12 06:46:02.995][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-12 06:46:02.996][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-12 06:46:02.998][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-12 06:46:02.999][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-12 06:46:03.000][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-12 06:46:03.002][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-12 06:46:03.003][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-12 06:46:03.004][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-12 06:46:03.005][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-12 06:46:03.007][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-12 06:46:03.008][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-12 06:46:03.009][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-12 06:46:03.010][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-12 06:46:03.011][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-12 06:46:03.013][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-12 06:46:03.014][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-12 06:46:03.015][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-12 06:46:03.016][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-12 06:46:03.018][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-12 06:46:03.019][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-12 06:46:03.020][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-12 06:46:03.022][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-12 06:46:03.023][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-12 06:46:03.024][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-12 06:46:03.026][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-12 06:46:03.027][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-12 06:46:03.028][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-12 06:46:03.030][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-12 06:46:03.031][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-12 06:46:03.032][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-12 06:46:03.033][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-12 06:46:03.035][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-12 06:46:03.036][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-12 06:46:03.037][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-12 06:46:03.039][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-12 06:46:03.040][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-12 06:46:03.041][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-12 06:46:03.042][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-12 06:46:03.044][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-12 06:46:03.045][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-12 06:46:03.046][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-12 06:46:03.047][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-12 06:46:03.048][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-12 06:46:03.050][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-12 06:46:03.051][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-12 06:46:03.052][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-12 06:46:03.053][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-12 06:46:03.054][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-12 06:46:03.056][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-12 06:46:03.057][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-12 06:46:03.058][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-12 06:46:03.059][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-12 06:46:03.061][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-12 06:46:03.062][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-12 06:46:03.063][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-12 06:46:03.064][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-12 06:46:03.065][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-12 06:46:03.066][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-12 06:46:03.068][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-12 06:46:03.069][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-12 06:46:03.070][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-12 06:46:03.071][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-12 06:46:03.073][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-12 06:46:03.075][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-12 06:46:03.076][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-12 06:46:03.077][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.080][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.115][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[2024-05-12 06:46:03.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.129][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[2024-05-12 06:46:03.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-12 06:46:03.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-12 06:46:03.165][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-12 06:46:03.166][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-12 06:46:03.168][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:03.169][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-12 06:46:03.170][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:03.171][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-12 06:46:03.172][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:03.173][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-12 06:46:03.173][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:03.174][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-12 06:46:03.175][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-12 06:46:03.176][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-12 06:46:03.177][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:03.177][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-12 06:46:03.178][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-12 06:46:03.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-12 06:46:03.187][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-12 06:46:03.188][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-12 06:46:03.188][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-12 06:46:03.188][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-12 06:46:03.189][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-12 06:46:03.190][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:03.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:03.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-12 06:46:03.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-12 06:46:03.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-12 06:46:03.193][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-12 06:46:03.194][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-12 06:46:03.194][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-12 06:46:03.195][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-12 06:46:03.196][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-12 06:46:03.196][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-12 06:46:03.197][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-12 06:46:03.197][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-12 06:46:03.198][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-12 06:46:03.200][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-12 06:46:03.201][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-12 06:46:03.203][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-12 06:46:03.204][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-12 06:46:03.205][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-12 06:46:03.208][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-12 06:46:03.209][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-12 06:46:03.210][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-12 06:46:03.212][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-12 06:46:03.213][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-12 06:46:03.214][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-12 06:46:03.215][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-12 06:46:03.216][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-12 06:46:03.217][biodb::testThat]
biodb.INFO [2024-05-12 06:46:03.218][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-05-12 06:46:03.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-12 06:46:03.219][biodb::testThat]
biodb.DEBUG[2024-05-12 06:46:03.222][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-12 06:46:03.226][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:03.227][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-12 06:46:03.228][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:03.230][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-12 06:46:03.233][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-12 06:46:03.237][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-12 06:46:03.238][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-12 06:46:03.239][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:03.241][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-05-12 06:46:03.245][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-05-12 06:46:03.246][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-12 06:46:03.248][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-05-12 06:46:03.250][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-12 06:46:03.253][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2024-05-12 06:46:03.254][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-12 06:46:03.255][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-12 06:46:03.256][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-12 06:46:03.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-12 06:46:03.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-12 06:46:03.273][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.274][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.276][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.281][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:46:03.282][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:46:03.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.283][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.311][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-12 06:46:03.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-12 06:46:03.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.315][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:46:03.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:46:03.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.318][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.320][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-12 06:46:03.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-12 06:46:03.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.323][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-12 06:46:03.324][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-12 06:46:03.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.326][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-12 06:46:03.328][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-12 06:46:03.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.330][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.331][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:03.332][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:03.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.333][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.335][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:03.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-12 06:46:03.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.338][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:46:03.339][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:46:03.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.341][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.342][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-12 06:46:03.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-12 06:46:03.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.345][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:03.346][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:03.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.348][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:03.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-12 06:46:03.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.352][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:03.353][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:03.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.355][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-12 06:46:03.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-12 06:46:03.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.360][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:46:03.361][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:46:03.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.362][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.364][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-12 06:46:03.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-12 06:46:03.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.367][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:46:03.368][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:46:03.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.370][ef$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.371][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-12 06:46:03.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-12 06:46:03.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:03.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:03.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:03.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:03.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-12 06:46:03.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-12 06:46:03.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-12 06:46:03.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-12 06:46:03.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-12 06:46:03.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-12 06:46:03.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-12 06:46:03.410][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-05-12 06:46:03.415][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-12 06:46:03.416][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-12 06:46:03.417][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-12 06:46:03.418][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-12 06:46:03.419][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-12 06:46:03.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-12 06:46:03.420][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-12 06:46:03.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-12 06:46:03.421][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-12 06:46:03.422][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".
[ 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
ChebiConn2.1310.8863.722
ChebiEntry0.3250.0170.352