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This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 197/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 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)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbChebi on lconway

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

raw results


Summary

Package: biodbChebi
Version: 1.11.0
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: 2024-06-24 18:55:36 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 18:57:38 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 122.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

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/meat/biodbChebi.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘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’
 OK
* 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: OK

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-x86_64/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


R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # 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 [2024-06-24 18:56:36.370][biodb::testContext]
biodb.INFO [2024-06-24 18:56:36.374][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 18:56:36.376][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-24 18:56:36.378][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 18:56:36.379][biodb::testContext]
biodb.INFO [2024-06-24 18:56:36.387][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-24 18:56:36.390][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 18:56:36.401][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:56:36.403][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 18:56:36.405][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 18:56:36.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.410][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 18:56:36.433][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 18:56:36.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.439][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 18:56:36.441][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 18:56:36.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.445][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 18:56:36.446][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 18:56:36.448][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 18:56:36.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.470][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 18:56:36.472][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 18:56:36.473][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 18:56:36.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.478][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 18:56:36.479][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 18:56:36.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.482][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[2024-06-24 18:56:36.482][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 18:56:36.483][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 18:56:36.484][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 18:56:36.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.489][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 18:56:36.491][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 18:56:36.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.495][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 18:56:36.496][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 18:56:36.497][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 18:56:36.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.501][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 18:56:36.502][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 18:56:36.504][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 18:56:36.505][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 18:56:36.506][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 18:56:36.507][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 18:56:36.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.511][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 18:56:36.512][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 18:56:36.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.517][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 18:56:36.518][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 18:56:36.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.522][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 18:56:36.523][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 18:56:36.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.528][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 18:56:36.529][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 18:56:36.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.532][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[2024-06-24 18:56:36.533][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 18:56:36.534][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 18:56:36.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.538][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 18:56:36.540][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 18:56:36.561][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 18:56:36.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.566][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 18:56:36.567][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 18:56:36.568][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 18:56:36.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.576][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 18:56:36.619][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.640][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 18:56:36.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:56:36.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.645][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.647][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 18:56:36.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:56:36.650][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.651][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 18:56:36.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:56:36.653][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.654][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.655][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:56:36.655][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:56:36.655][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:56:36.655][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 18:56:36.655][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 18:56:36.657][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:56:36.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:36.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:36.660][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:56:36.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:36.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:36.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.665][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:56:36.668][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:56:36.668][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.669][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.670][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 18:56:36.673][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.674][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 18:56:36.675][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.676][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:56:36.677][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.679][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.680][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.683][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 18:56:36.684][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:56:36.685][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.686][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 18:56:36.687][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:56:36.688][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.689][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.691][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:56:36.691][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:56:36.691][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:56:36.691][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 18:56:36.691][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 18:56:36.693][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:56:36.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:36.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:36.699][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:56:36.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:36.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:36.703][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.704][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.705][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:56:36.707][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:56:36.708][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.709][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.711][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 18:56:36.713][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.714][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 18:56:36.715][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.716][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:56:36.717][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.718][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.719][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.721][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.722][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 18:56:36.728][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:56:36.730][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.731][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 18:56:36.732][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:56:36.733][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.734][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.735][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.737][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:56:36.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:36.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:36.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:56:36.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:36.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:36.743][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.744][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:56:36.746][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:56:36.747][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.748][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.749][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 18:56:36.751][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.753][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 18:56:36.753][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.755][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:56:36.756][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.757][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.759][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.760][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.761][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 18:56:36.763][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:56:36.764][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.765][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 18:56:36.766][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:56:36.767][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.769][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:36.770][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.771][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:56:36.772][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:36.773][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:36.775][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:56:36.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:36.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:36.778][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:56:36.779][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.780][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:56:36.781][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:56:36.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:36.784][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:56:36.789][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:56:36.790][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.827][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[2024-06-24 18:56:36.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.839][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[2024-06-24 18:56:36.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.855][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[2024-06-24 18:56:36.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.866][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[2024-06-24 18:56:36.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:36.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:36.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:36.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:36.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:36.884][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 18:56:36.890][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 18:56:36.892][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 18:56:36.894][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 18:56:36.896][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 18:56:36.898][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 18:56:36.899][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 18:56:36.901][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 18:56:36.903][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 18:56:36.905][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 18:56:36.907][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 18:56:36.909][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 18:56:36.911][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 18:56:36.913][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 18:56:36.915][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 18:56:36.917][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 18:56:36.919][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 18:56:36.921][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 18:56:36.922][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 18:56:36.924][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 18:56:36.925][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 18:56:36.926][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 18:56:36.928][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 18:56:36.930][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 18:56:36.932][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 18:56:36.933][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 18:56:36.935][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 18:56:36.937][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 18:56:36.939][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 18:56:36.941][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 18:56:36.942][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 18:56:36.944][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 18:56:36.946][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 18:56:36.947][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 18:56:36.949][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 18:56:36.951][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 18:56:36.953][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 18:56:36.955][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 18:56:36.957][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 18:56:36.958][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 18:56:36.960][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 18:56:36.961][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 18:56:36.963][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 18:56:36.965][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 18:56:36.973][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 18:56:36.976][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 18:56:36.978][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 18:56:36.980][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 18:56:36.982][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 18:56:36.984][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 18:56:36.986][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 18:56:36.987][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 18:56:36.989][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 18:56:36.991][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 18:56:36.992][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 18:56:36.994][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 18:56:36.996][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 18:56:36.998][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 18:56:37.000][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 18:56:37.001][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 18:56:37.003][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 18:56:37.005][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 18:56:37.007][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 18:56:37.008][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 18:56:37.010][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 18:56:37.012][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 18:56:37.013][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 18:56:37.015][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 18:56:37.017][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 18:56:37.019][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 18:56:37.021][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 18:56:37.023][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 18:56:37.025][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 18:56:37.026][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 18:56:37.027][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 18:56:37.028][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 18:56:37.030][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 18:56:37.032][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 18:56:37.033][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 18:56:37.035][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 18:56:37.037][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 18:56:37.039][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 18:56:37.041][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 18:56:37.050][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 18:56:37.052][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-24 18:56:37.056][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:56:37.057][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.060][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.092][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[2024-06-24 18:56:37.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.100][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[2024-06-24 18:56:37.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.115][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[2024-06-24 18:56:37.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.129][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[2024-06-24 18:56:37.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.144][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[2024-06-24 18:56:37.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.158][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[2024-06-24 18:56:37.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:56:37.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:37.200][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 18:56:37.220][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 18:56:37.223][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:37.225][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 18:56:37.226][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:37.228][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:56:37.229][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:37.231][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:56:37.232][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:37.233][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 18:56:37.234][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 18:56:37.235][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:56:37.235][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:37.237][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 18:56:37.238][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 18:56:37.239][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 18:56:37.240][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 18:56:37.241][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:56:37.241][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:56:37.241][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:56:37.242][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 18:56:37.243][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:37.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:37.245][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:56:37.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:56:37.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:56:37.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:56:37.250][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:37.250][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 18:56:37.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:56:37.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:56:37.253][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 18:56:37.255][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 18:56:37.255][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 18:56:37.263][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 18:56:37.265][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 18:56:37.267][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 18:56:37.269][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 18:56:37.271][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 18:56:37.273][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 18:56:37.308][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 18:56:37.310][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 18:56:37.316][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 18:56:37.321][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 18:56:37.326][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 18:56:37.328][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 18:56:37.330][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 18:56:37.331][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 18:56:37.341][biodb::testThat]
biodb.INFO [2024-06-24 18:56:37.343][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-24 18:56:37.344][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:37.345][biodb::testThat]
biodb.TRACE[2024-06-24 18:56:37.350][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-06-24 18:56:37.353][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:37.357][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:37.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:37.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:37.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:37.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:37.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:37.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:37.390][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:56:37.403][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.405][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.408][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.432][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:37.433][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:37.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.436][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.469][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:37.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:37.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.474][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:37.476][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:37.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.478][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:37.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:37.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.484][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:37.496][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:37.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.499][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:37.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:37.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.506][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:37.508][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:37.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.510][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:37.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:37.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.517][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:37.519][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:37.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.521][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.523][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:37.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:37.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.528][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:37.529][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:37.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.532][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.533][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:37.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:37.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.539][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:37.540][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:37.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.543][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:37.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:37.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.550][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:37.551][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:37.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.553][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:37.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:37.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.561][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:37.562][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:37.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.565][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.566][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:37.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:37.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.570][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:37.572][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:37.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.574][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.576][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:37.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:37.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:37.669][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-06-24 18:56:37.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:37.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:37.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:37.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:37.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:37.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:37.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:37.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:37.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:37.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:37.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:37.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:37.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.763][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 18:56:37.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 18:56:37.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.767][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 18:56:37.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 18:56:37.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.771][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 18:56:37.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 18:56:37.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.775][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 18:56:37.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 18:56:37.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.901][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.904][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:37.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:37.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.942][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.943][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:37.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:37.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:37.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.969][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:37.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:37.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:37.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:37.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.979][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:37.980][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:37.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.983][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:37.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:37.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:37.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:37.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:38.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:38.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.005][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:38.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:38.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.008][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:38.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:38.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.012][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:38.013][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:38.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.015][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:38.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:38.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.046][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.047][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.049][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.078][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.079][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.081][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.095][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:38.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:38.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.100][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:38.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:38.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.105][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:38.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:38.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.109][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:38.115][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:38.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.117][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.118][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:38.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:38.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.132][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.136][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.141][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.146][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.147][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.149][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.151][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.165][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.170][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.175][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.179][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.180][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.182][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.183][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.195][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:38.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:38.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.203][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:38.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:38.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:38.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:38.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.214][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:38.215][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:38.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.219][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:38.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:38.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.250][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.251][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.253][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:38.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:38.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:38.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:38.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.276][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:38.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:38.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:38.280][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:38.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.283][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:38.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:38.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.300][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.301][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.304][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.311][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:38.318][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:38.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.320][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.326][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:38.327][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:38.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.336][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:38.337][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:38.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.339][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.345][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.347][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.350][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.356][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.358][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.360][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.366][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.368][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.371][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.377][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.379][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.381][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.387][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.392][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.399][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:38.400][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:38.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.402][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.410][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:38.411][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:38.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.414][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 18:56:38.427][biodb::testThat]
biodb.INFO [2024-06-24 18:56:38.428][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-24 18:56:38.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:38.431][biodb::testThat]
biodb.DEBUG[2024-06-24 18:56:38.449][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-06-24 18:56:38.458][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:38.464][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-06-24 18:56:38.466][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:56:38.468][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-06-24 18:56:38.470][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:38.495][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:38.496][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:38.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:38.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:38.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:38.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:38.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:38.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:38.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:38.513][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.514][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.516][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.548][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:38.549][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:38.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.551][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.553][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:38.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:38.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.557][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:38.558][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:38.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.561][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.563][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:38.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:38.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.568][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:38.569][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:38.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.571][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:38.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:38.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.576][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.577][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.579][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:38.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.585][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.586][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.588][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.589][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:38.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.594][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:38.595][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.597][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.598][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:38.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:38.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.602][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.605][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:38.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.610][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:38.611][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:38.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.613][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:38.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:38.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.619][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:38.620][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.622][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.623][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:38.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:38.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.628][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:38.629][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:38.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.631][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.632][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:38.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:38.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:38.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:38.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:38.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:38.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:38.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:38.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:38.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:38.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:38.684][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-06-24 18:56:38.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-24 18:56:38.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-24 18:56:38.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-24 18:56:38.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-24 18:56:38.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-24 18:56:38.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-24 18:56:38.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 18:56:38.717][biodb::testThat]
biodb.INFO [2024-06-24 18:56:38.719][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-24 18:56:38.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:38.722][biodb::testThat]
biodb.TRACE[2024-06-24 18:56:38.725][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:38.726][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:38.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.727][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:38.729][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-06-24 18:56:38.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:38.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:38.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:38.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:38.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:38.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:38.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:38.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:38.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:38.778][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-06-24 18:56:38.783][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 18:56:38.807][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:56:38.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 18:56:38.826][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:56:38.828][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 18:56:38.847][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:56:38.851][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:38.852][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:38.853][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:56:39.705][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:56:40.456][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:40.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-24 18:56:40.482][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-24 18:56:40.485][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-06-24 18:56:40.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:40.506][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:40.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.509][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.510][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.512][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.532][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 18:56:40.539][biodb::testThat]
biodb.INFO [2024-06-24 18:56:40.541][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-24 18:56:40.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:40.544][biodb::testThat]
biodb.TRACE[2024-06-24 18:56:40.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:40.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:40.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:40.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:40.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:40.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:40.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:40.653][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:56:40.658][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:56:40.660][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 18:56:40.662][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:56:40.664][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-06-24 18:56:40.694][biodb::testThat]
biodb.INFO [2024-06-24 18:56:40.696][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-24 18:56:40.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:40.697][biodb::testThat]
biodb.TRACE[2024-06-24 18:56:40.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:40.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:40.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:40.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:40.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:40.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:40.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:40.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:40.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 18:56:40.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 18:56:40.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.759][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 18:56:40.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 18:56:40.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.763][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 18:56:40.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 18:56:40.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.768][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 18:56:40.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 18:56:40.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:40.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:40.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:40.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:40.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:40.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:40.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:40.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:40.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:40.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.826][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 18:56:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 18:56:40.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 18:56:40.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 18:56:40.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.840][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 18:56:40.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 18:56:40.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 18:56:40.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 18:56:40.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:40.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 18:56:40.858][biodb::testThat]
biodb.INFO [2024-06-24 18:56:40.860][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-24 18:56:40.861][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:40.862][biodb::testThat]
biodb.INFO [2024-06-24 18:56:40.873][biodb::testThat]
biodb.INFO [2024-06-24 18:56:40.874][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-24 18:56:40.875][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:40.876][biodb::testThat]
biodb.INFO [2024-06-24 18:56:40.887][biodb::testThat]
biodb.INFO [2024-06-24 18:56:40.888][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-24 18:56:40.890][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:40.891][biodb::testThat]
biodb.DEBUG[2024-06-24 18:56:40.897][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-06-24 18:56:41.361][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-06-24 18:56:42.394][biodb::testThat]
biodb.INFO [2024-06-24 18:56:42.395][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-24 18:56:42.396][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:42.397][biodb::testThat]
biodb.DEBUG[2024-06-24 18:56:42.786][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[2024-06-24 18:56:43.171][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:43.173][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:43.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.175][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:43.176][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:43.177][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:43.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.178][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 18:56:43.180][biodb::testThat]
biodb.INFO [2024-06-24 18:56:43.181][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-24 18:56:43.182][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:56:43.183][biodb::testThat]
biodb.TRACE[2024-06-24 18:56:43.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:43.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:43.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:43.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:43.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:43.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:43.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:43.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:43.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:43.309][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:56:43.313][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:56:43.314][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 18:56:43.316][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:56:43.317][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 18:56:43.390][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:56:43.394][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:56:43.396][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 18:56:43.397][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:56:43.399][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-06-24 18:56:43.421][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 18:56:43.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 18:56:43.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:43.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:43.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:43.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:43.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:43.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:43.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:43.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:43.462][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:56:43.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:43.486][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:43.513][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:56:43.858][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:56:44.194][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:44.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-24 18:56:44.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-24 18:56:44.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:44.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:44.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:44.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:44.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:44.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:44.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:44.220][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-06-24 18:56:44.277][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:44.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-06-24 18:56:44.281][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:44.283][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:44.285][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:44.287][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:44.288][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:44.289][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:44.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:44.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:44.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:44.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:44.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:44.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:44.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:44.307][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-06-24 18:56:44.310][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:44.310][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:44.312][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-06-24 18:56:44.649][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-06-24 18:56:45.008][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:45.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-06-24 18:56:45.015][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-06-24 18:56:45.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-06-24 18:56:45.022][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:45.023][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:45.025][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:45.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:45.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:45.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:45.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:45.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:45.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:45.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:45.042][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.045][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.052][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:45.053][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:45.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.056][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.057][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:45.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:45.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.061][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:45.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:45.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.063][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.065][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:45.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:45.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.071][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:45.071][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:45.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.073][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:45.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:45.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.078][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:45.079][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:45.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.081][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:45.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:45.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.086][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:45.087][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:45.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.089][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.090][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:45.091][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:45.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.093][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.094][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:45.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:45.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:45.100][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:45.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:45.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:45.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.107][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:45.108][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:45.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:45.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:45.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.118][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:45.119][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:45.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.121][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.123][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:45.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:45.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.127][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:45.128][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:45.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.131][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.132][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:45.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:45.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:45.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:45.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:45.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:45.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:45.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:45.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:45.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:45.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:45.194][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-06-24 18:56:45.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:45.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:45.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:45.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:45.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:45.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:45.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:45.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:45.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:45.220][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:56:45.224][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:45.225][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:45.227][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:56:45.564][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:56:46.116][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:46.119][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-24 18:56:46.123][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-24 18:56:46.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:46.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:46.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:46.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:46.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:46.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:46.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:46.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:46.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:46.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:46.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:46.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:46.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:46.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:46.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:46.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:46.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:46.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:46.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:46.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:46.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:46.190][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-06-24 18:56:46.191][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:46.193][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-06-24 18:56:46.194][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:46.195][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:46.196][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:46.198][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:46.199][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:46.200][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:46.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:46.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:46.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:46.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:46.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:46.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:46.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:46.229][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-06-24 18:56:46.232][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:46.233][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:46.235][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-06-24 18:56:46.569][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-06-24 18:56:46.909][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:46.911][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-06-24 18:56:46.915][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-06-24 18:56:46.918][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-06-24 18:56:46.920][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:46.921][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:46.922][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:46.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:46.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:46.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:46.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:46.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:46.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:46.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:46.937][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:46.938][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:46.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.940][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:46.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:46.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.945][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:46.946][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:46.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.948][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.949][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:46.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:46.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.953][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:46.953][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:46.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.964][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:46.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:46.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.968][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:46.969][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:46.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.971][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:46.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:46.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.975][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:46.976][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:46.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:46.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:46.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.983][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:46.984][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:46.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.987][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:46.988][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:46.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.990][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.991][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:46.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:46.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:46.996][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:46.997][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:46.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:46.999][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:47.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:47.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.004][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:47.005][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:47.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.007][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:47.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.013][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:47.014][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:47.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.016][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.017][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:47.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:47.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:47.022][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:47.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.024][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:47.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:47.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:47.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:47.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:47.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:47.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:47.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:47.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:47.075][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-06-24 18:56:47.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:47.120][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:56:47.123][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:56:47.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 18:56:47.126][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:56:47.127][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 18:56:47.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:47.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:47.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:47.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:47.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:47.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:47.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:47.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:47.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:47.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:47.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:47.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:47.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:47.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:47.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:47.166][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-06-24 18:56:47.167][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:47.170][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-06-24 18:56:47.171][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:47.172][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:47.174][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:47.175][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:47.176][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:47.177][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:47.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:47.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:47.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:47.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:47.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:47.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:47.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:47.195][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-06-24 18:56:47.198][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:47.200][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:47.201][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-06-24 18:56:47.557][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-06-24 18:56:47.893][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:47.896][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-06-24 18:56:47.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-06-24 18:56:47.905][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-06-24 18:56:47.907][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:47.908][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:47.910][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:47.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:47.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:47.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:47.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:47.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:47.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:47.938][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.TRACE[2024-06-24 18:56:47.941][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.942][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.944][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:47.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:47.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.951][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:47.952][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:47.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.955][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.956][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:47.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:47.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.962][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:47.964][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:47.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.968][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:47.969][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:47.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.971][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.973][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:47.974][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:47.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.976][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.978][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:47.979][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:47.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.981][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:47.983][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:47.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.986][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:47.987][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:47.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.989][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.991][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:47.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:47.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:47.995][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:47.996][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:47.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:47.998][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.000][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:48.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:48.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.004][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:48.005][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:48.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.007][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:48.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:48.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:48.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:48.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:48.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:48.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:48.062][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-06-24 18:56:48.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:48.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:48.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:48.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:48.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:48.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:48.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:48.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:48.097][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-06-24 18:56:48.098][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:48.101][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-06-24 18:56:48.102][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:48.103][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:48.105][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:48.106][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:48.107][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:48.108][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:48.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:48.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:48.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:48.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:48.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:48.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:48.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:48.125][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-06-24 18:56:48.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:48.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:48.129][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-06-24 18:56:48.470][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-06-24 18:56:48.879][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:48.882][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-06-24 18:56:48.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-06-24 18:56:48.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-06-24 18:56:48.892][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:48.893][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:48.895][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:48.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:48.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:48.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:48.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:48.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:48.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:48.912][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:56:48.914][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.916][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.918][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:48.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:48.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.924][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:48.925][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:48.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.927][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.929][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:48.930][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:48.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.933][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.936][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:48.937][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:48.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.939][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.941][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:48.942][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:48.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.953][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.955][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:48.956][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:48.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.959][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.960][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:48.961][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:48.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.963][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.964][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:48.965][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:48.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.968][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.969][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:48.971][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:48.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:48.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:48.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.982][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:48.983][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:48.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.986][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.987][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:48.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:48.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.990][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:48.991][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:48.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.993][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:48.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:48.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:48.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:48.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:49.037][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-06-24 18:56:49.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:49.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:49.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:49.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:49.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:49.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:49.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:49.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:49.072][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-06-24 18:56:49.073][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:49.103][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-06-24 18:56:49.104][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:49.106][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:49.108][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:49.109][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:49.111][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:49.112][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:49.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:49.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:49.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:49.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:49.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:49.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:49.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:49.128][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-06-24 18:56:49.131][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:49.132][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:49.134][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-06-24 18:56:49.473][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-06-24 18:56:49.809][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:49.812][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-06-24 18:56:49.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-06-24 18:56:49.819][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-06-24 18:56:49.821][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:49.822][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:49.824][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:49.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:49.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:49.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:49.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:49.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:49.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:49.838][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:56:49.841][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.845][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.851][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:49.852][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:49.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.854][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.856][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:49.857][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:49.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.858][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.860][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:49.861][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:49.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.863][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.864][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:49.865][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:49.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.867][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:49.870][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:49.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.872][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.874][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:49.875][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.877][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.878][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:49.880][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:49.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.882][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.884][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:49.885][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:49.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.888][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:49.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:49.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.895][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:49.896][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:49.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.898][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.899][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:49.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:49.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.905][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:49.906][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:49.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.908][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:49.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:49.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:49.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:49.968][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-06-24 18:56:49.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:49.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:49.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:49.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:49.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:49.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:49.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:50.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:50.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:50.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:50.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:50.006][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-06-24 18:56:50.007][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:50.009][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-06-24 18:56:50.010][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:50.011][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:50.013][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:50.014][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:50.015][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:50.015][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:50.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:50.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:50.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:50.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:50.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:50.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:50.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:50.030][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-06-24 18:56:50.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:50.034][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:50.036][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-06-24 18:56:50.373][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-06-24 18:56:50.709][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:50.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-06-24 18:56:50.716][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-06-24 18:56:50.719][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-06-24 18:56:50.721][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:50.723][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:50.724][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:50.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:50.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:50.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:50.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:50.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:50.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:50.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:50.753][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.755][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.757][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.763][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:50.764][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:50.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.766][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.767][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:50.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:50.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.771][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:50.772][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:50.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.776][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:50.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:50.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.780][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:50.781][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:50.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.783][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:50.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:50.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.790][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:50.791][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:50.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.794][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:50.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:50.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.800][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:50.801][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:50.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.802][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.804][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:50.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:50.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.808][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:50.809][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:50.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.811][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:50.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:50.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.817][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:50.818][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:50.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.820][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:50.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:50.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.826][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:50.828][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:50.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.830][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:50.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:50.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.836][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:50.837][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:50.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.839][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.840][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:50.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:50.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.844][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:50.845][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:50.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.847][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.848][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:50.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:50.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:50.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:50.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:50.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:50.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:50.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:50.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:50.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:50.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:50.905][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-06-24 18:56:50.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:50.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:50.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:50.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:50.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:50.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:50.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:50.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:50.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:50.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:50.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:50.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:50.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:50.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:50.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:50.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:50.933][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-06-24 18:56:50.934][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:50.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-06-24 18:56:50.938][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:50.939][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:50.940][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:50.941][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:50.943][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:50.944][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:50.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:50.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:50.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:50.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:50.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:50.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:50.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:50.958][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-06-24 18:56:50.961][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:50.962][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:50.963][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-06-24 18:56:51.296][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-06-24 18:56:51.647][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:51.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-06-24 18:56:51.653][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-06-24 18:56:51.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-06-24 18:56:51.658][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:51.660][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:51.661][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:51.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:51.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:51.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:51.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:51.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:51.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:51.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:51.681][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.689][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.696][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.701][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:51.702][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:51.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.704][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.705][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:51.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:51.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.709][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:51.710][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:51.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.711][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:51.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:51.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.718][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:51.720][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:51.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.722][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:51.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:51.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.728][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:51.729][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:51.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.732][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:51.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:51.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.738][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:51.740][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:51.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.742][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.743][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:51.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:51.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.748][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:51.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:51.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.752][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.754][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:51.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:51.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.758][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:51.759][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:51.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.761][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:51.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:51.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.766][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:51.768][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:51.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.770][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:51.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:51.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:51.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:51.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.779][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.780][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:51.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:51.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.785][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:51.786][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:51.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.789][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:51.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:51.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:51.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:51.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:51.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:51.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:51.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:51.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:51.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:51.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:51.846][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-06-24 18:56:51.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:51.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:51.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:51.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:51.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:51.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:51.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:51.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:51.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:51.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:51.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:51.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:51.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:51.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:51.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:51.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:51.871][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-06-24 18:56:51.872][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:51.874][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-06-24 18:56:51.876][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:51.877][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:51.878][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:51.880][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:51.881][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:51.882][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:51.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:51.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:51.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:51.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:51.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:51.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:51.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:51.897][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-06-24 18:56:51.900][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:51.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:51.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-06-24 18:56:52.239][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-06-24 18:56:52.590][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:52.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-06-24 18:56:52.598][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-06-24 18:56:52.601][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-06-24 18:56:52.604][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:52.605][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:52.606][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:52.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:52.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:52.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:52.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:52.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:52.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:52.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:52.622][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.623][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.625][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.629][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:52.631][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:52.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.632][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.634][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:52.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:52.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.648][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:52.649][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:52.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.650][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:52.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:52.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.656][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:52.657][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:52.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.658][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:52.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:52.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.663][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:52.665][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:52.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.667][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:52.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:52.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.672][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:52.673][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:52.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.675][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.676][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:52.677][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:52.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.678][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.679][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:52.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:52.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.683][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:52.685][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:52.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:52.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.695][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:52.696][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:52.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.698][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:52.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:52.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.703][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:52.704][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:52.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.705][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.706][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:52.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:52.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.710][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:52.711][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:52.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.712][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.714][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:52.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:52.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:52.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:52.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:52.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:52.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:52.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:52.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:52.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:52.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:52.763][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-06-24 18:56:52.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:52.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:52.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:52.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:52.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:52.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:52.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:52.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:52.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:52.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:52.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:52.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:52.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:52.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:52.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:52.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:52.787][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-06-24 18:56:52.788][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:52.789][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-06-24 18:56:52.790][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:52.792][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:52.793][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:52.795][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:52.796][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:52.797][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:52.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:52.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:52.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:52.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:52.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:52.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:52.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:52.815][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-06-24 18:56:52.818][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:52.819][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:52.820][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-06-24 18:56:53.159][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-06-24 18:56:53.496][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:53.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-06-24 18:56:53.504][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-06-24 18:56:53.507][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-06-24 18:56:53.509][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:53.512][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:53.513][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:53.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:53.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:53.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:53.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:53.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:53.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:53.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:53.532][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.533][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.535][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.542][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:53.543][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:53.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.546][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.547][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:53.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:53.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.551][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:53.552][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:53.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.554][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.555][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:53.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:53.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.560][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:53.560][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:53.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.562][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:53.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:53.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.581][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:53.582][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:53.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.585][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:53.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:53.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.591][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:53.593][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:53.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.596][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.597][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:53.599][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:53.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.601][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.603][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:53.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:53.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.609][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:53.610][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:53.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.613][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:53.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.620][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:53.621][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:53.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.623][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:53.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:53.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.630][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:53.632][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:53.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.634][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.635][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:53.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:53.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.639][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:53.640][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:53.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.642][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.644][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:53.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:53.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:53.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:53.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:53.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:53.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:53.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:53.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:53.691][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-06-24 18:56:53.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:53.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:53.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:53.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:53.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:53.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:53.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:53.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:53.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:53.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:53.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:53.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:53.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:53.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:53.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:53.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:53.723][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-06-24 18:56:53.724][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:53.726][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-06-24 18:56:53.728][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:53.729][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:53.730][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:53.731][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:53.732][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:53.733][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:53.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:53.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:53.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:53.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:53.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:53.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:53.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:53.747][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-06-24 18:56:53.751][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:53.752][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:53.754][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-06-24 18:56:54.093][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-06-24 18:56:54.434][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:54.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-06-24 18:56:54.441][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-06-24 18:56:54.445][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-06-24 18:56:54.447][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:54.449][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:54.450][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:54.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:54.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:54.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:54.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:54.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:54.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:54.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:54.468][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.469][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.475][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:54.476][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:54.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.479][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.481][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:54.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:54.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.486][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:54.487][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:54.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.489][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:54.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:54.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.495][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:54.496][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:54.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.499][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.504][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:54.505][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:54.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.507][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:54.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:54.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.513][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:54.515][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:54.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.517][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.518][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:54.520][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:54.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.533][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.535][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:54.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:54.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.540][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:54.542][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:54.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.544][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:54.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:54.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.551][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:54.552][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:54.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.554][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:54.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:54.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.559][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:54.560][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:54.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.561][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.562][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:54.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:54.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.566][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:54.567][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:54.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.568][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:54.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:54.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:54.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:54.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:54.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:54.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:54.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:54.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:54.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:54.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:54.617][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-06-24 18:56:54.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:54.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:54.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:54.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:54.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:54.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:54.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:54.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:54.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:54.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:54.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:54.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:54.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:54.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:54.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:54.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:54.646][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-06-24 18:56:54.648][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:54.650][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-06-24 18:56:54.651][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:54.653][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:54.654][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:54.661][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:54.663][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:54.664][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:54.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:54.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:54.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:54.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:54.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:54.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:54.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:54.681][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-06-24 18:56:54.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:54.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:54.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-06-24 18:56:55.023][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-06-24 18:56:55.359][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:55.362][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-06-24 18:56:55.367][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-06-24 18:56:55.371][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-06-24 18:56:55.373][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:55.375][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:55.377][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:55.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:55.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:55.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:55.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:55.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:55.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:55.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:55.395][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.397][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.399][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.405][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:55.407][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:55.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.409][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.411][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:55.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:55.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.417][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:55.418][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:55.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.420][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:55.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.425][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:55.426][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:55.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.429][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:55.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:55.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.435][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:55.436][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:55.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.437][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:55.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:55.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.444][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:55.445][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:55.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.447][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.448][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:55.449][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:55.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.451][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.453][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:55.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:55.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.458][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:55.459][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:55.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.462][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:55.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:55.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.468][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:55.476][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:55.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.484][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:55.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:55.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.492][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:55.493][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:55.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.495][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:55.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.502][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:55.504][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:55.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.506][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.508][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:55.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:55.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:55.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:55.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:55.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:55.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:55.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:55.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:55.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:55.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:55.558][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-06-24 18:56:55.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:55.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:55.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:55.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:55.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:55.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:55.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:55.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:55.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:55.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:55.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:55.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:55.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:55.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:55.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:55.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:55.589][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-06-24 18:56:55.590][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:55.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-06-24 18:56:55.594][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:55.595][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:55.597][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:55.598][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:55.599][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:55.600][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:55.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:55.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:55.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:55.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:55.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:55.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:55.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:55.616][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-06-24 18:56:55.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:55.628][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:55.630][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-06-24 18:56:55.971][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-06-24 18:56:56.310][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:56.313][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-06-24 18:56:56.318][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-06-24 18:56:56.322][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-06-24 18:56:56.324][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:56.326][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:56.330][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:56.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:56.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:56.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:56.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:56.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:56.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:56.346][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:56:56.349][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.351][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.353][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.359][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:56.360][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:56.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.362][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.364][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:56.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:56.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.369][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:56.370][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:56.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.372][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.373][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:56.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:56.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.378][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:56.379][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:56.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.381][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:56.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:56.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.387][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:56.388][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:56.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.390][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:56.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:56.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.397][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:56.398][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:56.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.400][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.401][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:56.402][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:56.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.405][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.407][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:56.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:56.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.411][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:56.412][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:56.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:56.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:56.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.421][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:56.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:56.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.425][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:56.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:56.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.431][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:56.432][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:56.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.434][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.436][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:56.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:56.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.451][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:56.452][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:56.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.454][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.456][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:56.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:56.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:56.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:56.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:56.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:56.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:56.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:56.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:56.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:56.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:56.505][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-06-24 18:56:56.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:56.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:56.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:56.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:56.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:56.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:56.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:56.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:56.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:56.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:56.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:56.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:56.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:56.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:56.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:56.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:56.530][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-06-24 18:56:56.531][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:56.533][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-06-24 18:56:56.535][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:56.535][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:56.537][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:56.538][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:56.539][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:56.540][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:56.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:56.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:56.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:56.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:56.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:56.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:56.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:56.555][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-06-24 18:56:56.558][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:56.558][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:56.560][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-06-24 18:56:56.896][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-06-24 18:56:57.233][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:57.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-06-24 18:56:57.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-06-24 18:56:57.255][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-06-24 18:56:57.257][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:57.259][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:57.261][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:57.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:57.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:57.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:57.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:57.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:57.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:57.274][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:56:57.277][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.280][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.286][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:57.287][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:57.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.290][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:57.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:57.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.295][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:57.296][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:57.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.299][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:57.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:57.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.305][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:57.306][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:57.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.308][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.309][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:57.310][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:57.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.312][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.313][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:57.314][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:57.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.316][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.317][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:57.318][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:57.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.320][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.321][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:57.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:57.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.325][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:57.326][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:57.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.327][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:57.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:57.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.332][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:57.333][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:57.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.336][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:57.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:57.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.341][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:57.342][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:57.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.344][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.346][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:57.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:57.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.349][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:57.350][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:57.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.352][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:57.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:57.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:57.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:57.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:57.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:57.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:57.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:57.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:57.401][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-06-24 18:56:57.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:57.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:57.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:57.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:57.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:57.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:57.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:57.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:57.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:57.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:57.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:57.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:57.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:57.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:57.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:57.428][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-06-24 18:56:57.429][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:57.430][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-06-24 18:56:57.431][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:57.432][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:57.433][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:57.434][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:57.435][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:57.436][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:57.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:57.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:57.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:57.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:57.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:57.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:57.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:57.451][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-06-24 18:56:57.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:57.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:57.456][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-06-24 18:56:57.793][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-06-24 18:56:58.129][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:58.132][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-06-24 18:56:58.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-06-24 18:56:58.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-06-24 18:56:58.141][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:58.143][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:58.144][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:58.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:58.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:58.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:58.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:58.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:58.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:58.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:58.160][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.161][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.163][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.169][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:58.179][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:58.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.181][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.183][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:58.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:58.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.186][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:58.187][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:58.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:58.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:58.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.194][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:58.195][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:58.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.197][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.198][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:58.200][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:58.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.202][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.203][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:58.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:58.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.206][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.208][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:58.209][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:58.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.212][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:58.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:58.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.216][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:58.217][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:58.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.218][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:58.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:58.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.224][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:58.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:58.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.227][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:58.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:58.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.233][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:58.234][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:58.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.236][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.238][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:58.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:58.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.242][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:58.243][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:58.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.245][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:58.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:58.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:58.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:58.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:58.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:58.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:58.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:58.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:58.284][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-06-24 18:56:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:58.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:58.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:58.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:58.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:58.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:58.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:58.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:58.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:58.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:58.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:58.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:58.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:58.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:58.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:58.316][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-06-24 18:56:58.317][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:58.319][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-06-24 18:56:58.320][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:58.321][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:58.322][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:58.323][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:58.324][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:58.325][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:58.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:58.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:58.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:58.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:58.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:58.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:58.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:58.341][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-06-24 18:56:58.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:58.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:58.347][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-06-24 18:56:58.684][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-06-24 18:56:59.022][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:59.025][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-06-24 18:56:59.030][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-06-24 18:56:59.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-06-24 18:56:59.035][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:59.036][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:59.037][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:59.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:59.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:59.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:59.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:59.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:59.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:59.051][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:56:59.054][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.056][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.058][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.064][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:59.065][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:59.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.066][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.067][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:59.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:59.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.071][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:59.072][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:59.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.074][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:59.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:59.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.078][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:59.079][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:59.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.081][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:59.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:59.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.085][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:59.086][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:59.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:59.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:59.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.101][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:59.102][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:59.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.103][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.105][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:59.105][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:59.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.107][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.108][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:59.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:59.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.112][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:59.113][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:59.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.114][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:59.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:56:59.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.119][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:59.120][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:59.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.121][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:56:59.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:56:59.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.126][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:59.127][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:59.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.129][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.131][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:56:59.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:56:59.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.137][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:59.138][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:59.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.139][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.141][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:56:59.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:56:59.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:59.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:59.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:59.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:56:59.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:56:59.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:59.183][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-06-24 18:56:59.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:59.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:59.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:59.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:59.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:59.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:56:59.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:56:59.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:59.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:59.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:59.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:59.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:59.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:59.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:59.215][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-06-24 18:56:59.216][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:56:59.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-06-24 18:56:59.220][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:56:59.221][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:56:59.222][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:56:59.223][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:56:59.224][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:56:59.225][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:56:59.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:59.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:59.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:59.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:59.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:59.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:59.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:56:59.242][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-06-24 18:56:59.244][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:56:59.245][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:56:59.247][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-06-24 18:56:59.581][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-06-24 18:56:59.916][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:56:59.919][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-06-24 18:56:59.923][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-06-24 18:56:59.926][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-06-24 18:56:59.927][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:56:59.928][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:56:59.929][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:56:59.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:56:59.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:56:59.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:56:59.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:56:59.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:56:59.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:56:59.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:56:59.944][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.945][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.947][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:56:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:56:59.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.953][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:59.954][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:59.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.955][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.957][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:56:59.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:56:59.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.960][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:59.961][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:59.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.963][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.964][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:56:59.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:56:59.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.968][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:59.969][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:59.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.971][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:56:59.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:56:59.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.976][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:59.977][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:59.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.979][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:56:59.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:56:59.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.984][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:59.985][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:56:59.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:56:59.986][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:56:59.987][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:56:59.988][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.001][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.003][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:00.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.007][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:00.008][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:00.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:00.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:00.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.015][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:00.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:00.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.017][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:00.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:00.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.023][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:00.024][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:00.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.027][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:00.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:00.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.030][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:00.031][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:00.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.033][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.034][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:00.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:00.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:00.082][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-06-24 18:57:00.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:00.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:00.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:00.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:00.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:00.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:00.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:00.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:00.109][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-06-24 18:57:00.110][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:00.111][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-06-24 18:57:00.112][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:00.113][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:00.114][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:00.124][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:00.125][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:00.127][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:00.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:00.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:00.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:00.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:00.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:00.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:00.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:00.142][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-06-24 18:57:00.144][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:00.145][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:00.147][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-06-24 18:57:00.482][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-06-24 18:57:00.846][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:00.848][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-06-24 18:57:00.852][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-06-24 18:57:00.856][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-06-24 18:57:00.859][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:00.861][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:00.862][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:00.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:00.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:00.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:00.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:00.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:00.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:00.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:00.879][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.881][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.883][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:00.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:00.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.889][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:00.890][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:00.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.893][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:00.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:00.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.899][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:00.900][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:00.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.903][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:00.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:00.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.908][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:00.910][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:00.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.912][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:00.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:00.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.919][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:00.920][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:00.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.923][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:00.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:00.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.929][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:00.930][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:00.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.932][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.934][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:00.935][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.937][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.939][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:00.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:00.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.943][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:00.944][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:00.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:00.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:00.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.952][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:00.964][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:00.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:00.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:00.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.974][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:00.975][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:00.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.978][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:00.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:00.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.982][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:00.983][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:00.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.986][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.987][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:00.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:00.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:00.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:00.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:00.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:01.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:01.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:01.038][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-06-24 18:57:01.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:01.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:01.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:01.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:01.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:01.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:01.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:01.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:01.065][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-06-24 18:57:01.066][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:01.067][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-06-24 18:57:01.069][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:01.070][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:01.072][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:01.073][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:01.074][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:01.075][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:01.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:01.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:01.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:01.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:01.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:01.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:01.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:01.098][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-06-24 18:57:01.102][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:01.103][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:01.104][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-06-24 18:57:01.439][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-06-24 18:57:01.783][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-06-24 18:57:01.786][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-24 18:57:01.788][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-06-24 18:57:01.795][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-06-24 18:57:01.798][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-06-24 18:57:01.800][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:01.802][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:01.803][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:01.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:01.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:01.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:01.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:01.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:01.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:01.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:01.826][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.827][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.830][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.835][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:01.836][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:01.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.838][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.840][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:01.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:01.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.845][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:01.847][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:01.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:01.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:01.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.856][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:01.857][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:01.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.859][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:01.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:01.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.866][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:01.867][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:01.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.870][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:01.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:01.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.876][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:01.877][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:01.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.880][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.881][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:01.882][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.885][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.886][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:01.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.892][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:01.894][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:01.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.896][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:01.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:01.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.902][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:01.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:01.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:01.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:01.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.913][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:01.914][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:01.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.916][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.917][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:01.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:01.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.930][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:01.932][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:01.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.935][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.936][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:01.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:01.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:01.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:01.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:01.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:01.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:01.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:01.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:01.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:01.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:01.992][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-06-24 18:57:01.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:01.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:01.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:01.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:02.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:02.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:02.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:02.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:02.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:02.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:02.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:02.020][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-06-24 18:57:02.021][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:02.022][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-06-24 18:57:02.024][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:02.028][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:02.029][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:02.031][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:02.032][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:02.033][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:02.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:02.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:02.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:02.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:02.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:02.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:02.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:02.053][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-06-24 18:57:02.057][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:02.058][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:02.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-06-24 18:57:02.395][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-06-24 18:57:02.745][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:02.748][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-06-24 18:57:02.762][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-06-24 18:57:02.771][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-06-24 18:57:02.773][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:02.776][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:02.778][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:02.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:02.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:02.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:02.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:02.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:02.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:02.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:02.796][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.797][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.799][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.805][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:02.806][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:02.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.809][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.811][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:02.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:02.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.815][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:02.816][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:02.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.818][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.819][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:02.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:02.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.824][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:02.825][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:02.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.826][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:02.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:02.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.833][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:02.835][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:02.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.837][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:02.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:02.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.844][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:02.845][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:02.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.848][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.850][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:02.851][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.853][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.855][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:02.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.861][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:02.861][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:02.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.864][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:02.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:02.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.871][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:02.872][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:02.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.874][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:02.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:02.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.880][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:02.881][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:02.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.883][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.884][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:02.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:02.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.887][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:02.889][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:02.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:02.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:02.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:02.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:02.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:02.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:02.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:02.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:02.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:02.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:02.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:02.959][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-06-24 18:57:02.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:02.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:02.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:02.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:02.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:02.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:02.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:02.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:02.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:02.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:02.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:02.984][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-06-24 18:57:02.986][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:02.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-06-24 18:57:02.990][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:02.991][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:02.993][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:02.994][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:02.996][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:02.997][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:03.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:03.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:03.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:03.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:03.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:03.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:03.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:03.014][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-06-24 18:57:03.018][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:03.020][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:03.022][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-06-24 18:57:03.363][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-06-24 18:57:03.699][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:03.701][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-06-24 18:57:03.705][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-06-24 18:57:03.708][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-06-24 18:57:03.709][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:03.711][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:03.712][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:03.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:03.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:03.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:03.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:03.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:03.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:03.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:03.738][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.740][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.742][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.749][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:03.750][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:03.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.752][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.753][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:03.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:03.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.757][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:03.758][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:03.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.761][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.763][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:03.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:03.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.768][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:03.769][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:03.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.771][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:03.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:03.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.779][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:03.781][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:03.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.783][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:03.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:03.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.789][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:03.790][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:03.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.791][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.793][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:03.795][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:03.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.797][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.799][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:03.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:03.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.804][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:03.805][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:03.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.807][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:03.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:03.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.814][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:03.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:03.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.817][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:03.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:03.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.824][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:03.826][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:03.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.828][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.829][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:03.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:03.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.835][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:03.836][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:03.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.839][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.841][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:03.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:03.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:03.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:03.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:03.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:03.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:03.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:03.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:03.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:03.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:03.906][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-06-24 18:57:03.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:03.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:03.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:03.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:03.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:03.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:03.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:03.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:03.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:03.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:03.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:03.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:03.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:03.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:03.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:03.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:03.936][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-06-24 18:57:03.937][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:03.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-06-24 18:57:03.941][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:03.942][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:03.944][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:03.945][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:03.946][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:03.947][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:03.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:03.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:03.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:03.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:03.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:03.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:03.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:03.962][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-06-24 18:57:03.965][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:03.967][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:03.969][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-06-24 18:57:04.306][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-06-24 18:57:04.642][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:04.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-06-24 18:57:04.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-06-24 18:57:04.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-06-24 18:57:04.660][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:04.662][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:04.663][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:04.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:04.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:04.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:04.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:04.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:04.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:04.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:04.681][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.682][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.684][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.701][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:04.703][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:04.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.706][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.708][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:04.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:04.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.713][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:04.715][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:04.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.718][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:04.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.724][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:04.725][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:04.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.728][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:04.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:04.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.735][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:04.736][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:04.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.738][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:04.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:04.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.743][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:04.744][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:04.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.745][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.746][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:04.748][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:04.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.750][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.751][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:04.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:04.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.756][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:04.757][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:04.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.759][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:04.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:04.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.765][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:04.766][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:04.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.768][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:04.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:04.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:04.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:04.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.779][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.780][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:04.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:04.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.785][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:04.786][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:04.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.789][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:04.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:04.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:04.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:04.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:04.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:04.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:04.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:04.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:04.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:04.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:04.847][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-06-24 18:57:04.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:04.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:04.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:04.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:04.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:04.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:04.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:04.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:04.888][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:04.892][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:04.893][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:04.895][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:05.369][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:05.848][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-06-24 18:57:05.850][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-24 18:57:05.852][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-24 18:57:05.856][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-24 18:57:05.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:05.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:05.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:05.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:05.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:05.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:05.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:05.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:05.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:05.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:05.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:05.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:05.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:05.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:05.895][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:05.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:05.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:05.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:05.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:05.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:05.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:05.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:05.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:05.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:05.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:05.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:05.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:05.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:05.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:05.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:05.972][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:05.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:05.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:05.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:05.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:05.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:05.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:05.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.003][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:06.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:06.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:06.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.094][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:06.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:06.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.149][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:06.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.179][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:06.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:06.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.240][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:06.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.267][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:06.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.294][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.TRACE[2024-06-24 18:57:06.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:06.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:06.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.376][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.TRACE[2024-06-24 18:57:06.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.402][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:06.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:06.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:06.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:06.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:06.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:06.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:06.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:06.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:06.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:06.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:06.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:06.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:06.526][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:06.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:06.531][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:06.533][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:06.876][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:07.211][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:07.214][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-06-24 18:57:07.218][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-06-24 18:57:07.222][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:07.226][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:07.228][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:07.229][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:07.566][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:07.905][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:07.908][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-06-24 18:57:07.913][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-06-24 18:57:07.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:07.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:07.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:07.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:07.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:07.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:07.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:07.929][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-06-24 18:57:07.930][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:07.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-06-24 18:57:07.934][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:07.935][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:07.936][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:07.937][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:07.949][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:07.950][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:07.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:07.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:07.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:07.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:07.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:07.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:07.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:07.966][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-06-24 18:57:07.969][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:07.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:07.972][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-06-24 18:57:08.327][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-06-24 18:57:08.661][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:08.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-06-24 18:57:08.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-06-24 18:57:08.670][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-06-24 18:57:08.672][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:08.673][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:08.674][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:08.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:08.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:08.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:08.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:08.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:08.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:08.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:08.691][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.692][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.694][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.699][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:08.700][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:08.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.702][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.703][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:08.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:08.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.707][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:08.708][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:08.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.710][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:08.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:08.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.716][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:08.717][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:08.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.718][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:08.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:08.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.723][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:08.725][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:08.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.727][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:08.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.733][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:08.734][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:08.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.736][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.737][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:08.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:08.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.741][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:08.742][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:08.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.744][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.746][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:08.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:08.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.751][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.752][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.762][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.774][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:08.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:08.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.778][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.780][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:08.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:08.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.785][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:08.786][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:08.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.789][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.790][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:08.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.795][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:08.795][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:08.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.799][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:08.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:08.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:08.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:08.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:08.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:08.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:08.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:08.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:08.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:08.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:08.851][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-06-24 18:57:08.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:08.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:08.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:08.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:08.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:08.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:08.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:08.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:08.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:08.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:08.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:08.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:08.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:08.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:08.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:08.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:08.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:08.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:08.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:08.915][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-06-24 18:57:08.916][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:08.918][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-06-24 18:57:08.920][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:08.921][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:08.922][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:08.924][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:08.925][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:08.926][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:08.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:08.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:08.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:08.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:08.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:08.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:08.939][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[2024-06-24 18:57:08.941][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-06-24 18:57:08.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:08.945][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:08.946][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-06-24 18:57:09.281][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-06-24 18:57:09.619][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:09.622][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-06-24 18:57:09.627][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-06-24 18:57:09.630][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-06-24 18:57:09.632][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:09.633][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:09.635][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:09.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:09.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:09.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:09.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:09.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:09.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:09.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:09.650][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.651][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.653][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.658][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:09.659][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:09.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.661][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.663][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:09.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:09.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.667][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:09.669][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:09.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.670][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.671][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:09.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:09.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.676][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:09.677][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:09.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.680][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:09.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:09.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.687][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:09.688][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:09.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.690][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:09.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:09.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.695][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:09.696][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:09.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.705][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.711][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:09.713][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:09.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.716][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.718][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:09.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:09.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.723][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.725][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.727][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.732][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:09.733][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:09.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.735][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:09.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:09.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.742][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:09.743][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:09.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.745][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.746][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:09.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:09.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.751][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:09.752][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:09.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.755][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.756][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:09.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:09.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:09.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:09.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:09.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:09.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:09.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:09.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:09.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:09.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:09.810][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-06-24 18:57:09.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:09.858][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:09.862][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:09.863][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 18:57:09.865][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:09.867][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 18:57:09.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:09.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:09.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:09.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:09.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:09.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:09.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:09.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:09.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:09.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:09.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:09.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:09.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:09.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:09.911][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:09.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:09.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:09.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:09.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:09.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:09.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:09.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:09.952][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:09.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:09.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:09.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:09.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:09.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:09.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:09.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:09.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:09.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:09.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.175][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.240][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.267][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.295][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.322][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.TRACE[2024-06-24 18:57:10.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.349][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.TRACE[2024-06-24 18:57:10.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.378][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[2024-06-24 18:57:10.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.410][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.507][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.TRACE[2024-06-24 18:57:10.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.565][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.598][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.665][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.709][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:10.713][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:10.716][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 18:57:10.718][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:10.720][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 18:57:10.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.765][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.797][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.897][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.TRACE[2024-06-24 18:57:10.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:10.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.951][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:10.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:10.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:10.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:10.978][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:10.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:10.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:10.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:10.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:10.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:10.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:10.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:11.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.033][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:11.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:11.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.094][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:11.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:11.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:11.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:11.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:11.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.244][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:11.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.274][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:11.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:11.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:11.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.334][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 18:57:11.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 18:57:11.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 18:57:11.352][biodb::testThat]
biodb.INFO [2024-06-24 18:57:11.353][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-24 18:57:11.354][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:11.355][biodb::testThat]
biodb.TRACE[2024-06-24 18:57:11.358][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 18:57:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 18:57:11.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:11.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:11.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:11.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:11.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:11.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:11.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:11.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:11.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:11.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:11.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:11.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:11.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:11.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:11.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:11.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:11.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:11.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:11.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:11.406][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:11.407][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:11.410][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:11.759][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:12.097][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:12.099][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-24 18:57:12.103][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-24 18:57:12.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:12.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:12.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:12.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:12.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:12.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:12.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:12.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:12.132][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:12.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:12.136][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:12.139][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:12.478][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:12.812][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:12.814][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-24 18:57:12.818][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-24 18:57:12.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:12.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:12.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:12.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:12.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:12.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:12.831][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.TRACE[2024-06-24 18:57:12.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:12.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:12.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:12.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:12.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:12.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:12.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:12.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:12.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:12.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:12.877][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 18:57:12.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:12.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:12.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:12.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:12.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:12.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:12.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:12.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.900][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:12.901][private$selectFields]
biodb.TRACE[2024-06-24 18:57:12.902][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:12.903][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:12.904][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:12.905][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.906][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.908][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.909][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.910][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.912][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.913][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:12.914][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:12.915][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.916][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.918][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.918][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:12.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.937][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 18:57:12.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:12.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:12.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:12.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:12.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:12.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:12.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:12.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:12.959][private$selectFields]
biodb.TRACE[2024-06-24 18:57:12.960][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:12.961][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:12.961][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:12.962][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.964][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.965][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.966][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.967][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.969][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.970][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:12.971][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:12.972][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.973][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.975][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.976][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:12.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:12.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:12.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:12.988][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 18:57:12.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:12.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:12.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:12.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:12.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:12.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:13.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:13.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:13.012][private$selectFields]
biodb.TRACE[2024-06-24 18:57:13.014][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:13.015][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:13.016][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:13.017][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.021][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.022][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.023][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.025][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:13.027][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:13.027][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.029][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.030][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.031][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:13.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:13.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.043][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 18:57:13.044][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 18:57:13.045][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 18:57:13.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:13.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:13.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:13.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:13.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:13.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:13.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:13.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:13.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:13.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:13.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:13.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:13.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:13.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:13.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:13.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:13.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:13.135][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[2024-06-24 18:57:13.138][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:13.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:13.142][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:13.143][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:13.484][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:13.830][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:13.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-24 18:57:13.837][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-24 18:57:13.842][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:13.845][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:13.846][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:13.848][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:14.210][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:14.548][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:14.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-24 18:57:14.555][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-24 18:57:14.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:14.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:14.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:14.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:14.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:14.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:14.570][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.TRACE[2024-06-24 18:57:14.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:14.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:14.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:14.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:14.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:14.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:14.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:14.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:14.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:14.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:14.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:14.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:14.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:14.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:14.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:14.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:14.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:14.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:14.666][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 18:57:14.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:14.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:14.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:14.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:14.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:14.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:14.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:14.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.710][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.711][private$selectFields]
biodb.TRACE[2024-06-24 18:57:14.711][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:14.712][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:14.714][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.718][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.718][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.719][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.721][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.722][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.723][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.724][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.725][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.728][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.729][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:14.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.743][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 18:57:14.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:14.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:14.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:14.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:14.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:14.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:14.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:14.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.797][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.798][private$selectFields]
biodb.TRACE[2024-06-24 18:57:14.799][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:14.800][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:14.800][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.801][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.803][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.804][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.805][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.806][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.808][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.809][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.822][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.823][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.825][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.827][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.829][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:14.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.840][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 18:57:14.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:14.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:14.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:14.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:14.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:14.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:14.852][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:14.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.862][private$selectFields]
biodb.TRACE[2024-06-24 18:57:14.863][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:14.864][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:14.865][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.867][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.869][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.870][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.871][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.873][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.875][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.875][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:14.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.878][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.880][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:14.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:14.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.896][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 18:57:14.897][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 18:57:14.898][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 18:57:14.908][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 18:57:14.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 18:57:14.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 18:57:14.918][biodb::testThat]
biodb.INFO [2024-06-24 18:57:14.919][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-24 18:57:14.920][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:14.921][biodb::testThat]
biodb.TRACE[2024-06-24 18:57:14.924][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 18:57:14.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 18:57:14.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:14.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:14.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:14.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:14.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:14.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:14.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:14.960][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[2024-06-24 18:57:14.963][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:14.967][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:14.968][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-24 18:57:14.969][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:14.971][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-24 18:57:14.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:14.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:14.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:14.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:14.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:14.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:14.985][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:14.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:14.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:14.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:14.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:14.999][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:15.002][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:15.003][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-24 18:57:15.004][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:15.006][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-24 18:57:15.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.018][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:15.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.043][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:15.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.056][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 18:57:15.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.070][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.TRACE[2024-06-24 18:57:15.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.078][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.079][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.080][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.083][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.084][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.085][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.087][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.089][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.091][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.092][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.093][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.094][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.095][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.107][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 18:57:15.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.128][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.128][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.129][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.130][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.132][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.134][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.136][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.137][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.138][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.139][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.140][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.141][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.144][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.144][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.158][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 18:57:15.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.168][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.177][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.178][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.179][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.180][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.180][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.181][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.183][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.185][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.186][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.187][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.190][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.190][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.191][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.193][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.194][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.195][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.207][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 18:57:15.208][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 18:57:15.209][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 18:57:15.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:15.258][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:15.261][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:15.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-24 18:57:15.263][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:15.264][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-24 18:57:15.267][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:15.270][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:15.271][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-24 18:57:15.272][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:15.273][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-24 18:57:15.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.287][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:15.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.346][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:15.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.361][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 18:57:15.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.372][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.TRACE[2024-06-24 18:57:15.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.384][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.385][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.386][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.387][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.388][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.389][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.391][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.393][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.395][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.395][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.396][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.397][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.400][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.400][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.412][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 18:57:15.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.431][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.432][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.434][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.435][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.435][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.436][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.437][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.440][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.441][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.442][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.443][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.444][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.449][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.463][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 18:57:15.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.488][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.489][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.490][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.492][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.493][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.495][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.496][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.499][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.501][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.502][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.502][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.504][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.505][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.521][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 18:57:15.522][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 18:57:15.523][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 18:57:15.533][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 18:57:15.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 18:57:15.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 18:57:15.543][biodb::testThat]
biodb.INFO [2024-06-24 18:57:15.544][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-24 18:57:15.545][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:15.546][biodb::testThat]
biodb.TRACE[2024-06-24 18:57:15.548][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 18:57:15.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 18:57:15.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:15.584][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:15.587][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:15.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-24 18:57:15.590][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:15.591][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-24 18:57:15.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.622][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:15.626][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:15.628][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-24 18:57:15.630][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:15.632][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-24 18:57:15.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.647][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:15.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.669][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:15.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:15.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.682][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 18:57:15.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.713][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.714][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.715][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.716][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.717][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.718][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.720][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.722][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.723][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.724][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.726][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.727][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.728][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.730][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.732][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.733][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.746][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 18:57:15.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.768][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.770][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.770][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.771][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.773][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.774][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.776][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.777][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.778][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.779][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.781][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.782][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.782][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.783][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.785][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.786][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.798][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 18:57:15.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.819][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.820][private$selectFields]
biodb.TRACE[2024-06-24 18:57:15.822][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:15.823][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:15.824][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.825][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.826][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.829][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.830][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.831][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.832][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.833][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.834][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:15.835][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.836][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.837][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.838][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:15.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.849][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 18:57:15.850][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 18:57:15.851][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 18:57:15.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:15.912][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:15.915][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:15.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-24 18:57:15.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:15.921][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-24 18:57:15.924][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:15.928][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:15.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-24 18:57:15.931][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:15.933][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-24 18:57:15.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:15.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.970][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.TRACE[2024-06-24 18:57:15.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:15.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:15.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:15.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:15.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:15.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:15.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:15.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:15.995][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:15.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:15.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:15.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:16.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:16.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:16.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:16.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:16.009][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 18:57:16.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:16.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:16.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:16.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:16.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:16.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:16.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:16.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.028][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.029][private$selectFields]
biodb.TRACE[2024-06-24 18:57:16.030][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:16.031][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:16.032][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.032][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.033][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.035][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.036][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.037][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.038][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.039][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.040][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.041][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.042][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.044][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.045][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:16.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.063][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 18:57:16.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:16.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:16.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:16.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:16.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:16.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:16.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:16.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.082][private$selectFields]
biodb.TRACE[2024-06-24 18:57:16.083][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:16.084][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:16.085][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.087][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.088][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.089][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.090][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.092][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.093][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.097][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.098][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:16.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.110][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 18:57:16.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:16.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:16.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:16.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:16.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:16.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:16.121][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.TRACE[2024-06-24 18:57:16.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.129][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.129][private$selectFields]
biodb.TRACE[2024-06-24 18:57:16.130][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 18:57:16.131][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 18:57:16.132][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.133][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.134][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.135][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.136][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.138][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.140][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.141][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.142][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 18:57:16.143][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.144][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.147][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 18:57:16.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.162][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 18:57:16.163][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 18:57:16.164][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 18:57:16.186][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 18:57:16.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 18:57:16.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 18:57:16.194][biodb::testThat]
biodb.INFO [2024-06-24 18:57:16.195][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-24 18:57:16.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:16.197][biodb::testThat]
biodb.DEBUG[2024-06-24 18:57:16.199][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-24 18:57:16.200][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:16.201][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-24 18:57:16.203][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:16.204][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:16.205][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:16.206][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:16.206][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:16.207][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:16.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:16.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:16.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:16.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:16.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:16.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:16.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:16.221][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-06-24 18:57:16.223][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:16.224][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:16.225][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-06-24 18:57:16.564][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-06-24 18:57:16.909][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:16.912][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-06-24 18:57:16.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-06-24 18:57:16.921][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-06-24 18:57:16.924][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:16.925][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:16.926][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:16.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:16.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:16.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:16.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:16.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:16.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:16.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:16.943][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:16.944][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:16.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:16.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:16.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.951][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:16.952][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:16.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.954][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.955][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:16.956][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:16.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.958][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.959][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:16.960][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:16.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.962][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.963][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:16.964][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:16.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.967][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:16.968][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:16.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.972][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:16.973][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:16.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.976][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.977][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:16.978][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:16.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.982][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:16.983][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:16.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.986][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:16.987][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:16.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.988][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.990][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:16.991][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:16.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.993][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:16.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:16.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:17.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:17.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:17.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:17.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:17.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:17.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:17.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:17.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:17.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:17.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:17.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:17.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:17.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:17.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:17.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:17.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:17.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:17.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:17.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:17.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:17.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:17.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:17.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:17.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:17.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:17.030][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-06-24 18:57:17.031][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-24 18:57:17.042][biodb::testThat]
biodb.INFO [2024-06-24 18:57:17.043][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-24 18:57:17.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:17.046][biodb::testThat]
biodb.DEBUG[2024-06-24 18:57:17.058][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-06-24 18:57:17.059][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-06-24 18:57:17.060][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-06-24 18:57:17.062][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-06-24 18:57:17.063][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-06-24 18:57:17.064][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:17.065][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:17.066][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:17.067][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:17.067][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:17.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:17.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:17.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:17.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:17.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:17.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:17.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:17.083][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-06-24 18:57:17.087][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:17.088][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:17.089][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-06-24 18:57:17.433][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-06-24 18:57:17.775][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:17.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-06-24 18:57:17.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-06-24 18:57:17.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:17.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:17.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:17.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:17.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:17.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:17.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:17.813][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-06-24 18:57:17.816][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:17.817][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:17.818][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-06-24 18:57:18.159][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-06-24 18:57:18.498][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:18.500][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-06-24 18:57:18.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-06-24 18:57:18.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:18.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:18.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:18.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:18.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:18.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:18.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:18.520][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-06-24 18:57:18.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:18.523][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:18.525][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-06-24 18:57:18.861][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-06-24 18:57:19.211][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:19.214][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-06-24 18:57:19.218][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-06-24 18:57:19.221][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-06-24 18:57:19.223][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:19.224][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-06-24 18:57:19.225][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:19.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:19.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:19.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:19.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:19.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:19.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:19.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:19.239][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.240][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.241][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.246][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:19.247][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:19.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.249][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.250][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:19.251][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:19.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.253][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.254][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:19.255][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:19.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.257][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.258][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.259][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.261][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.262][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.262][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.264][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.265][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:19.266][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:19.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.268][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.269][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.270][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.271][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.272][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:19.273][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:19.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.275][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.276][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:19.277][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:19.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.279][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.280][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:19.281][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:19.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.283][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:19.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:19.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:19.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:19.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:19.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:19.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:19.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:19.324][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.327][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.332][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:19.333][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:19.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.335][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.336][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:19.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:19.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.339][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:19.340][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:19.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.342][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.343][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:19.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:19.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.347][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:19.348][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:19.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.349][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:19.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:19.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.354][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.355][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.361][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.362][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.364][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.365][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.369][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:19.370][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:19.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.372][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.374][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:19.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:19.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.378][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.379][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.380][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.386][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:19.387][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:19.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.389][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:19.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:19.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.394][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:19.395][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:19.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.397][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.399][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:19.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:19.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.404][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:19.405][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:19.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.407][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.408][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:19.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:19.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:19.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:19.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:19.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:19.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:19.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:19.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:19.455][FUN] Functions in observer BiodbConfig: [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[2024-06-24 18:57:19.458][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.459][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.460][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.466][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:19.467][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:19.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.469][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.470][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:19.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:19.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.475][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:19.476][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:19.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.478][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:19.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:19.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.484][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:19.485][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:19.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.487][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:19.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:19.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.493][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.494][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.496][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:19.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.502][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.502][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.504][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.506][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:19.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.509][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:19.510][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:19.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.512][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:19.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:19.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.530][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.531][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.533][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:19.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.537][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:19.538][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:19.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.540][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:19.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:19.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.544][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:19.545][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:19.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.546][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.548][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:19.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:19.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.551][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:19.552][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:19.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.553][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.554][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:19.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:19.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:19.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:19.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:19.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:19.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:19.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:19.613][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-06-24 18:57:19.614][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-24 18:57:19.614][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-06-24 18:57:19.629][biodb::testThat]
biodb.INFO [2024-06-24 18:57:19.631][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-24 18:57:19.632][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:19.633][biodb::testThat]
biodb.INFO [2024-06-24 18:57:19.660][biodb::testThat]
biodb.INFO [2024-06-24 18:57:19.661][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-24 18:57:19.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:19.663][biodb::testThat]
biodb.INFO [2024-06-24 18:57:19.673][biodb::testThat]
biodb.INFO [2024-06-24 18:57:19.675][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-24 18:57:19.676][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:19.677][biodb::testThat]
biodb.DEBUG[2024-06-24 18:57:19.679][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[2024-06-24 18:57:19.682][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:19.683][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:19.685][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:20.078][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:20.550][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:20.553][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-06-24 18:57:20.557][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-06-24 18:57:20.570][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:20.571][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:20.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:20.573][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:20.574][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:20.575][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:20.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:20.577][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 18:57:20.578][biodb::testThat]
biodb.INFO [2024-06-24 18:57:20.579][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-24 18:57:20.580][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:20.581][biodb::testThat]
biodb.ERROR[2024-06-24 18:57:20.595][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-24 18:57:20.610][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-24 18:57:20.623][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 18:57:20.625][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 18:57:20.626][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 18:57:20.627][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 18:57:20.629][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:20.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:20.630][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.632][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 18:57:20.643][biodb::testContext]
biodb.INFO [2024-06-24 18:57:20.644][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 18:57:20.645][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-06-24 18:57:20.646][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 18:57:20.647][biodb::testContext]
biodb.INFO [2024-06-24 18:57:20.649][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-24 18:57:20.650][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 18:57:20.654][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:20.655][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 18:57:20.656][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 18:57:20.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.658][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[2024-06-24 18:57:20.659][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 18:57:20.660][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 18:57:20.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.663][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 18:57:20.664][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 18:57:20.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.667][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 18:57:20.668][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 18:57:20.669][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 18:57:20.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.672][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 18:57:20.673][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 18:57:20.674][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 18:57:20.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.677][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 18:57:20.678][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 18:57:20.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.681][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 18:57:20.682][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 18:57:20.683][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 18:57:20.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.686][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 18:57:20.687][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 18:57:20.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.690][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 18:57:20.691][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 18:57:20.692][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 18:57:20.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.694][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[2024-06-24 18:57:20.695][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 18:57:20.696][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 18:57:20.697][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 18:57:20.698][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 18:57:20.699][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 18:57:20.700][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 18:57:20.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.704][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 18:57:20.705][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 18:57:20.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.708][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[2024-06-24 18:57:20.709][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 18:57:20.710][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 18:57:20.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.715][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 18:57:20.716][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 18:57:20.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.728][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 18:57:20.730][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 18:57:20.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.733][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 18:57:20.733][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 18:57:20.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.736][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[2024-06-24 18:57:20.736][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 18:57:20.737][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 18:57:20.757][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 18:57:20.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.761][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 18:57:20.762][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 18:57:20.763][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 18:57:20.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.766][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[2024-06-24 18:57:20.767][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 18:57:20.768][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.769][self$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[2024-06-24 18:57:20.770][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.771][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:20.772][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.772][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.773][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.774][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.775][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 18:57:20.776][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:20.777][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.777][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 18:57:20.778][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:20.779][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.781][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:20.781][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:20.781][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:20.781][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 18:57:20.781][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 18:57:20.782][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:20.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:20.784][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:20.784][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:20.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:20.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:20.787][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.788][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.788][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:20.789][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:20.790][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.791][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.792][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 18:57:20.794][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.795][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 18:57:20.796][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.797][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:20.798][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.799][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.800][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.801][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.802][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 18:57:20.803][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:20.803][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.804][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 18:57:20.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:20.806][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.807][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.807][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:20.807][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:20.807][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:20.807][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 18:57:20.807][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 18:57:20.808][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:20.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:20.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:20.811][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:20.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:20.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:20.814][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.815][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.816][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:20.816][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:20.817][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.818][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.819][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 18:57:20.821][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.822][self$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[2024-06-24 18:57:20.823][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.824][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:20.824][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.825][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.826][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.827][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.828][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 18:57:20.829][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:20.830][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.831][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 18:57:20.832][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:20.833][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.834][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.835][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.836][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:20.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:20.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:20.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:20.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:20.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:20.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.842][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.842][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:20.843][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:20.844][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.845][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.846][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 18:57:20.848][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.848][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 18:57:20.849][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.850][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:20.851][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.852][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.853][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.854][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.855][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 18:57:20.856][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:20.857][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.858][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 18:57:20.859][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:20.860][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.861][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:20.862][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.863][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:20.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:20.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:20.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:20.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:20.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:20.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:20.868][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.869][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:20.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:20.871][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:20.872][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:20.874][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:20.874][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:20.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:20.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:20.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:20.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:20.949][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 18:57:20.951][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 18:57:20.952][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 18:57:20.953][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 18:57:20.955][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 18:57:20.956][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 18:57:20.957][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 18:57:20.958][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 18:57:20.960][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 18:57:20.961][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 18:57:20.962][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 18:57:20.964][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 18:57:20.965][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 18:57:20.966][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 18:57:20.967][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 18:57:20.968][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 18:57:20.970][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 18:57:20.971][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 18:57:20.972][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 18:57:20.973][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 18:57:20.975][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 18:57:20.976][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 18:57:20.977][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 18:57:20.978][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 18:57:20.980][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 18:57:20.981][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 18:57:20.982][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 18:57:20.983][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 18:57:20.985][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 18:57:20.986][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 18:57:20.987][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 18:57:20.988][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 18:57:20.990][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 18:57:20.991][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 18:57:20.992][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 18:57:20.993][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 18:57:20.995][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 18:57:20.996][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 18:57:20.997][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 18:57:20.998][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 18:57:21.000][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 18:57:21.001][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 18:57:21.002][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 18:57:21.003][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 18:57:21.005][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 18:57:21.006][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 18:57:21.007][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 18:57:21.008][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 18:57:21.010][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 18:57:21.011][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 18:57:21.012][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 18:57:21.014][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 18:57:21.015][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 18:57:21.016][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 18:57:21.017][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 18:57:21.018][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 18:57:21.019][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 18:57:21.021][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 18:57:21.022][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 18:57:21.023][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 18:57:21.025][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 18:57:21.026][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 18:57:21.027][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 18:57:21.028][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 18:57:21.030][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 18:57:21.031][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 18:57:21.032][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 18:57:21.033][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 18:57:21.035][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 18:57:21.036][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 18:57:21.037][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 18:57:21.039][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 18:57:21.040][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 18:57:21.041][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 18:57:21.042][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 18:57:21.044][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 18:57:21.045][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 18:57:21.054][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 18:57:21.055][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 18:57:21.056][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 18:57:21.058][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 18:57:21.059][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 18:57:21.060][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 18:57:21.061][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 18:57:21.063][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-24 18:57:21.064][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:21.065][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.067][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.089][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[2024-06-24 18:57:21.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.114][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[2024-06-24 18:57:21.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.121][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[2024-06-24 18:57:21.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.139][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[2024-06-24 18:57:21.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.157][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[2024-06-24 18:57:21.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.163][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[2024-06-24 18:57:21.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:21.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:21.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:21.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:21.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:21.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:21.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:21.172][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 18:57:21.173][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 18:57:21.175][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:21.176][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 18:57:21.177][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:21.179][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:21.180][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:21.181][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:21.182][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:21.183][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 18:57:21.185][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 18:57:21.186][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:21.187][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:21.188][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 18:57:21.189][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 18:57:21.190][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 18:57:21.192][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:21.193][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:21.193][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:21.193][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:21.194][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 18:57:21.195][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:21.196][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:21.197][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:21.198][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:21.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:21.200][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:21.201][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:21.201][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 18:57:21.202][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:21.202][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:21.203][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:21.204][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 18:57:21.204][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 18:57:21.206][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 18:57:21.207][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 18:57:21.208][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 18:57:21.210][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 18:57:21.212][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 18:57:21.213][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 18:57:21.216][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 18:57:21.217][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 18:57:21.218][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 18:57:21.220][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 18:57:21.221][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 18:57:21.222][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 18:57:21.223][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 18:57:21.224][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 18:57:21.225][biodb::testThat]
biodb.INFO [2024-06-24 18:57:21.226][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-06-24 18:57:21.227][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:21.228][biodb::testThat]
biodb.DEBUG[2024-06-24 18:57:21.231][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 18:57:21.234][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:21.235][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:21.236][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-06-24 18:57:21.565][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-06-24 18:57:22.057][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:22.059][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-06-24 18:57:22.063][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-06-24 18:57:22.067][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[2024-06-24 18:57:22.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:22.072][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:22.073][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:22.424][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:22.760][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:22.762][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-06-24 18:57:22.768][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-06-24 18:57:22.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:22.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:22.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:22.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:22.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:22.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:22.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:22.786][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:22.790][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:22.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:22.793][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:23.178][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:23.529][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:23.531][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-06-24 18:57:23.536][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-06-24 18:57:23.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:23.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:23.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:23.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:23.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:23.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:23.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:23.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:23.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:23.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:23.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:23.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:23.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:23.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:23.583][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[2024-06-24 18:57:23.586][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:23.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-24 18:57:23.589][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:23.591][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-24 18:57:23.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:23.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:23.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:23.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:23.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:23.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:23.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:23.606][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[2024-06-24 18:57:23.610][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:23.612][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-24 18:57:23.613][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:23.615][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-24 18:57:23.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:23.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:23.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:23.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:23.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:23.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:23.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:23.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:23.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:23.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:23.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:23.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:23.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:23.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:23.658][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[2024-06-24 18:57:23.662][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:23.663][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-24 18:57:23.665][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:23.666][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-24 18:57:23.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:23.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:23.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:23.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:23.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:23.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:23.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:23.681][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[2024-06-24 18:57:23.684][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:23.685][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-24 18:57:23.687][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:23.688][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-24 18:57:23.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:23.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:23.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:23.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:23.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:23.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:23.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:23.702][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[2024-06-24 18:57:23.705][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:23.706][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:23.707][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:24.043][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:24.390][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:24.393][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-06-24 18:57:24.397][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-06-24 18:57:24.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:24.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:24.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:24.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:24.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:24.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:24.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 18:57:24.418][biodb::testThat]
biodb.INFO [2024-06-24 18:57:24.419][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-06-24 18:57:24.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:24.422][biodb::testThat]
biodb.DEBUG[2024-06-24 18:57:24.425][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:24.428][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:24.429][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:24.432][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:24.770][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:25.106][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:25.108][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-06-24 18:57:25.114][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-06-24 18:57:25.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:25.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:25.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:25.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:25.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:25.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.129][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[2024-06-24 18:57:25.134][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[2024-06-24 18:57:25.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:25.139][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:25.142][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:25.492][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:25.829][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:25.831][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-06-24 18:57:25.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-06-24 18:57:25.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:25.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:25.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:25.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:25.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:25.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 18:57:25.858][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 18:57:25.859][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 18:57:25.861][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 18:57:25.862][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 18:57:25.863][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:25.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:25.865][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:25.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:25.867][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 18:57:25.871][biodb::testContext]
biodb.INFO [2024-06-24 18:57:25.872][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 18:57:25.873][biodb::testContext] Test context - Test web services
biodb.INFO [2024-06-24 18:57:25.874][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 18:57:25.875][biodb::testContext]
biodb.INFO [2024-06-24 18:57:25.878][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-24 18:57:25.879][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 18:57:25.884][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:25.885][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 18:57:25.886][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 18:57:25.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.890][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 18:57:25.890][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 18:57:25.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.894][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 18:57:25.895][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 18:57:25.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.897][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[2024-06-24 18:57:25.898][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 18:57:25.899][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 18:57:25.901][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 18:57:25.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.905][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 18:57:25.906][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 18:57:25.907][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 18:57:25.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.912][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 18:57:25.913][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 18:57:25.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.916][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 18:57:25.917][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 18:57:25.918][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 18:57:25.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.922][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 18:57:25.923][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 18:57:25.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.928][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 18:57:25.929][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 18:57:25.930][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 18:57:25.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.935][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 18:57:25.935][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 18:57:25.936][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 18:57:25.937][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 18:57:25.938][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 18:57:25.939][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 18:57:25.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.943][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 18:57:25.944][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 18:57:25.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.946][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[2024-06-24 18:57:25.947][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 18:57:25.948][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 18:57:25.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.952][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 18:57:25.953][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 18:57:25.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.956][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 18:57:25.957][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 18:57:25.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.962][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 18:57:25.962][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 18:57:25.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.966][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 18:57:25.967][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 18:57:25.990][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 18:57:25.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:25.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:25.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:25.995][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 18:57:25.996][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 18:57:25.997][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 18:57:25.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.002][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 18:57:26.004][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.005][self$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[2024-06-24 18:57:26.007][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.008][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:26.009][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.009][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.010][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.011][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.012][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 18:57:26.013][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:26.014][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.014][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 18:57:26.015][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:26.016][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.017][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.018][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:26.018][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:26.018][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:26.018][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 18:57:26.018][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 18:57:26.019][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:26.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.020][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.021][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:26.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.024][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.025][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.026][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:26.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:26.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.028][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.029][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 18:57:26.031][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.032][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 18:57:26.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:26.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.036][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.037][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.038][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 18:57:26.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:26.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.041][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 18:57:26.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:26.042][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.044][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.045][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:26.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:26.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:26.045][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 18:57:26.045][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 18:57:26.046][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:26.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.049][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:26.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.053][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.054][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.055][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:26.056][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:26.057][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.058][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.060][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 18:57:26.062][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.063][self$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[2024-06-24 18:57:26.064][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.065][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:26.067][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.068][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.069][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.070][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.071][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 18:57:26.072][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:26.074][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.075][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 18:57:26.076][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:26.077][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.078][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.080][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.081][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:26.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.100][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:26.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.104][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.105][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.106][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:26.107][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:26.107][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.108][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.109][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 18:57:26.111][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.112][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 18:57:26.113][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.113][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:26.114][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.115][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.116][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.117][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.117][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 18:57:26.118][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:26.119][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.120][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 18:57:26.121][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:26.122][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.122][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.124][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.124][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:26.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.127][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:26.128][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.131][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.132][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:26.134][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:26.134][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.135][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:26.137][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:26.137][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.148][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[2024-06-24 18:57:26.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.152][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[2024-06-24 18:57:26.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.160][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[2024-06-24 18:57:26.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.185][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[2024-06-24 18:57:26.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.215][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 18:57:26.217][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 18:57:26.218][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 18:57:26.220][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 18:57:26.222][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 18:57:26.223][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 18:57:26.225][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 18:57:26.226][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 18:57:26.227][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 18:57:26.228][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 18:57:26.229][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 18:57:26.231][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 18:57:26.232][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 18:57:26.233][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 18:57:26.234][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 18:57:26.235][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 18:57:26.236][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 18:57:26.238][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 18:57:26.240][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 18:57:26.241][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 18:57:26.242][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 18:57:26.243][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 18:57:26.245][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 18:57:26.246][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 18:57:26.247][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 18:57:26.248][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 18:57:26.249][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 18:57:26.251][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 18:57:26.252][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 18:57:26.253][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 18:57:26.255][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 18:57:26.256][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 18:57:26.257][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 18:57:26.258][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 18:57:26.260][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 18:57:26.261][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 18:57:26.262][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 18:57:26.264][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 18:57:26.265][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 18:57:26.267][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 18:57:26.268][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 18:57:26.270][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 18:57:26.271][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 18:57:26.272][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 18:57:26.273][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 18:57:26.275][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 18:57:26.276][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 18:57:26.277][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 18:57:26.279][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 18:57:26.280][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 18:57:26.281][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 18:57:26.283][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 18:57:26.284][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 18:57:26.285][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 18:57:26.286][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 18:57:26.287][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 18:57:26.288][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 18:57:26.289][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 18:57:26.291][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 18:57:26.292][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 18:57:26.293][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 18:57:26.294][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 18:57:26.295][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 18:57:26.296][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 18:57:26.298][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 18:57:26.299][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 18:57:26.300][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 18:57:26.302][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 18:57:26.303][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 18:57:26.305][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 18:57:26.306][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 18:57:26.307][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 18:57:26.309][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 18:57:26.310][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 18:57:26.311][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 18:57:26.313][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 18:57:26.314][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 18:57:26.316][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 18:57:26.318][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 18:57:26.319][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 18:57:26.321][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 18:57:26.322][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 18:57:26.323][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 18:57:26.324][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 18:57:26.326][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-24 18:57:26.327][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:26.328][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.330][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.337][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[2024-06-24 18:57:26.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.353][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[2024-06-24 18:57:26.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:26.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:26.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:26.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:26.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:26.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:26.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:26.447][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 18:57:26.448][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 18:57:26.449][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.451][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.452][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.453][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:26.454][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.455][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.456][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.456][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 18:57:26.457][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 18:57:26.458][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:26.459][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.460][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 18:57:26.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 18:57:26.462][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 18:57:26.463][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:26.464][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:26.464][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:26.464][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:26.465][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 18:57:26.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.468][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:26.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:26.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:26.470][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:26.471][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:26.471][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 18:57:26.472][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:26.473][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:26.474][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:26.475][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 18:57:26.475][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 18:57:26.476][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 18:57:26.478][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 18:57:26.479][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 18:57:26.481][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 18:57:26.482][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 18:57:26.484][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 18:57:26.487][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 18:57:26.488][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 18:57:26.489][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 18:57:26.490][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 18:57:26.491][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 18:57:26.493][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 18:57:26.494][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 18:57:26.495][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 18:57:26.496][biodb::testThat]
biodb.INFO [2024-06-24 18:57:26.497][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-06-24 18:57:26.498][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:26.499][biodb::testThat]
biodb.DEBUG[2024-06-24 18:57:26.502][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 18:57:26.506][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:26.507][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 18:57:26.509][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:26.510][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 18:57:26.513][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 18:57:26.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:26.518][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:26.520][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 18:57:26.858][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 18:57:27.196][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:27.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-24 18:57:27.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-06-24 18:57:27.215][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 18:57:27.217][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 18:57:27.219][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 18:57:27.220][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 18:57:27.221][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.223][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.225][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.225][FUN] Functions in observer BiodbConfig: [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 [2024-06-24 18:57:27.229][biodb::testContext]
biodb.INFO [2024-06-24 18:57:27.230][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 18:57:27.231][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-06-24 18:57:27.233][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 18:57:27.233][biodb::testContext]
biodb.INFO [2024-06-24 18:57:27.236][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-24 18:57:27.238][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 18:57:27.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:27.243][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 18:57:27.244][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 18:57:27.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.248][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 18:57:27.249][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 18:57:27.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.254][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 18:57:27.255][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 18:57:27.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.259][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 18:57:27.260][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 18:57:27.261][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 18:57:27.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.266][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 18:57:27.266][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 18:57:27.268][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 18:57:27.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.271][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 18:57:27.272][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 18:57:27.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.275][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 18:57:27.276][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 18:57:27.277][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 18:57:27.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.280][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 18:57:27.281][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 18:57:27.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.285][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 18:57:27.285][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 18:57:27.286][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 18:57:27.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.290][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 18:57:27.291][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 18:57:27.293][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 18:57:27.295][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 18:57:27.296][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 18:57:27.298][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 18:57:27.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.302][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 18:57:27.303][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 18:57:27.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.306][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 18:57:27.307][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 18:57:27.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.311][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 18:57:27.312][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 18:57:27.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.316][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 18:57:27.317][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 18:57:27.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.322][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 18:57:27.324][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 18:57:27.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.327][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 18:57:27.328][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 18:57:27.353][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 18:57:27.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.356][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[2024-06-24 18:57:27.358][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 18:57:27.358][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 18:57:27.360][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 18:57:27.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.363][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 18:57:27.365][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.366][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 18:57:27.366][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.367][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:27.368][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.369][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.370][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.371][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.372][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 18:57:27.373][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:27.374][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.375][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 18:57:27.376][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:27.377][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.377][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.379][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:27.379][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:27.379][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:27.379][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 18:57:27.379][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 18:57:27.379][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:27.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:27.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.387][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:27.389][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:27.390][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.391][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.392][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 18:57:27.394][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.395][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 18:57:27.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.397][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:27.398][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.399][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.400][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.401][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.402][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 18:57:27.402][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:27.403][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.405][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 18:57:27.406][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:27.407][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.408][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.410][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:27.410][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:27.410][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:27.410][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 18:57:27.410][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 18:57:27.411][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:27.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.414][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:27.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.418][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.419][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.420][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:27.421][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:27.422][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.423][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.425][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 18:57:27.427][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.428][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 18:57:27.429][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.430][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:27.431][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.432][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.433][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.434][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.436][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 18:57:27.437][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:27.438][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.439][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 18:57:27.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:27.440][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.441][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.442][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.444][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:27.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:27.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.450][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.451][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:27.453][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:27.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.454][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.455][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 18:57:27.457][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.458][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 18:57:27.459][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.460][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:27.461][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.462][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.474][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.475][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 18:57:27.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:27.477][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.478][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 18:57:27.480][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:27.481][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.482][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.483][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 18:57:27.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.486][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:27.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.489][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.490][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:27.492][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:27.493][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.494][self$setPropertyValue]
biodb.DEBUG[2024-06-24 18:57:27.495][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:27.496][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.518][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[2024-06-24 18:57:27.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.522][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[2024-06-24 18:57:27.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.527][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[2024-06-24 18:57:27.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.532][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[2024-06-24 18:57:27.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.570][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 18:57:27.571][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 18:57:27.572][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 18:57:27.573][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 18:57:27.575][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 18:57:27.576][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 18:57:27.578][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 18:57:27.580][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 18:57:27.581][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 18:57:27.582][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 18:57:27.583][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 18:57:27.585][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 18:57:27.586][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 18:57:27.587][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 18:57:27.589][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 18:57:27.590][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 18:57:27.591][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 18:57:27.593][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 18:57:27.594][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 18:57:27.595][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 18:57:27.596][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 18:57:27.597][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 18:57:27.599][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 18:57:27.600][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 18:57:27.601][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 18:57:27.602][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 18:57:27.604][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 18:57:27.605][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 18:57:27.606][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 18:57:27.607][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 18:57:27.608][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 18:57:27.610][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 18:57:27.611][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 18:57:27.612][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 18:57:27.613][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 18:57:27.614][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 18:57:27.616][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 18:57:27.617][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 18:57:27.619][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 18:57:27.620][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 18:57:27.621][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 18:57:27.623][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 18:57:27.624][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 18:57:27.626][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 18:57:27.627][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 18:57:27.628][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 18:57:27.630][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 18:57:27.631][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 18:57:27.633][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 18:57:27.634][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 18:57:27.635][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 18:57:27.637][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 18:57:27.638][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 18:57:27.639][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 18:57:27.641][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 18:57:27.642][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 18:57:27.643][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 18:57:27.644][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 18:57:27.646][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 18:57:27.647][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 18:57:27.649][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 18:57:27.650][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 18:57:27.651][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 18:57:27.653][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 18:57:27.654][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 18:57:27.655][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 18:57:27.657][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 18:57:27.658][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 18:57:27.660][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 18:57:27.661][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 18:57:27.663][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 18:57:27.665][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 18:57:27.666][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 18:57:27.668][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 18:57:27.669][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 18:57:27.671][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 18:57:27.673][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 18:57:27.674][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 18:57:27.675][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 18:57:27.677][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 18:57:27.678][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 18:57:27.680][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 18:57:27.682][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 18:57:27.684][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 18:57:27.687][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-24 18:57:27.688][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 18:57:27.689][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.691][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.699][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[2024-06-24 18:57:27.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.720][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[2024-06-24 18:57:27.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.733][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[2024-06-24 18:57:27.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.762][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[2024-06-24 18:57:27.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 18:57:27.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.806][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 18:57:27.807][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 18:57:27.809][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.810][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.811][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.812][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 18:57:27.813][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.815][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.816][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 18:57:27.817][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 18:57:27.819][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 18:57:27.820][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.821][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 18:57:27.822][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 18:57:27.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 18:57:27.824][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 18:57:27.825][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 18:57:27.825][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 18:57:27.825][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 18:57:27.826][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 18:57:27.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.828][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 18:57:27.829][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 18:57:27.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 18:57:27.831][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 18:57:27.831][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:27.831][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 18:57:27.832][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 18:57:27.833][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 18:57:27.835][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 18:57:27.836][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 18:57:27.836][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 18:57:27.838][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 18:57:27.840][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 18:57:27.842][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 18:57:27.843][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 18:57:27.845][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 18:57:27.847][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 18:57:27.850][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 18:57:27.851][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 18:57:27.852][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 18:57:27.853][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 18:57:27.855][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 18:57:27.855][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 18:57:27.857][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 18:57:27.857][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 18:57:27.859][biodb::testThat]
biodb.INFO [2024-06-24 18:57:27.860][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-06-24 18:57:27.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 18:57:27.861][biodb::testThat]
biodb.DEBUG[2024-06-24 18:57:27.864][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 18:57:27.867][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:27.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 18:57:27.870][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:27.871][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 18:57:27.874][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[2024-06-24 18:57:27.876][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 18:57:27.878][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-06-24 18:57:27.879][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 18:57:27.880][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-06-24 18:57:27.884][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-06-24 18:57:27.885][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 18:57:27.887][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-06-24 18:57:27.888][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 18:57:27.889][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 18:57:27.890][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 18:57:27.891][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 18:57:27.892][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 18:57:27.893][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 18:57:27.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:27.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:27.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:27.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:27.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:27.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:27.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 18:57:27.909][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-06-24 18:57:27.912][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 18:57:27.914][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 18:57:27.915][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-06-24 18:57:28.259][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-06-24 18:57:29.389][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 18:57:29.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-06-24 18:57:29.398][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-06-24 18:57:29.402][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-06-24 18:57:29.405][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 18:57:29.407][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 18:57:29.408][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 18:57:29.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 18:57:29.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:29.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:29.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:29.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:29.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:29.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 18:57:29.427][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.428][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.430][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.437][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:29.438][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:29.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.440][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.441][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 18:57:29.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 18:57:29.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.446][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:29.447][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:29.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 18:57:29.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 18:57:29.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.453][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 18:57:29.454][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 18:57:29.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.456][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.457][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 18:57:29.458][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 18:57:29.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.460][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.461][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:29.463][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:29.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.465][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.467][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:29.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 18:57:29.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.471][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:29.472][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:29.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.474][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.475][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 18:57:29.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 18:57:29.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.479][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:29.480][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:29.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.483][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:29.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 18:57:29.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.489][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:29.490][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:29.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.492][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 18:57:29.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 18:57:29.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.499][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:29.500][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:29.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.502][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.503][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 18:57:29.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 18:57:29.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.509][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:29.510][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:29.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.512][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 18:57:29.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 18:57:29.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:29.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:29.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:29.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 18:57:29.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 18:57:29.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 18:57:29.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 18:57:29.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 18:57:29.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 18:57:29.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 18:57:29.566][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-06-24 18:57:29.574][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 18:57:29.576][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 18:57:29.577][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 18:57:29.578][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 18:57:29.579][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 18:57:29.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 18:57:29.581][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 18:57:29.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 18:57:29.583][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 18:57:29.584][FUN] Functions in observer 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 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 19.801   1.211  55.611

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.5670.9054.544
ChebiEntry0.4020.0170.499